24.10.0p2

(12th of December 2024)

• (E/P) Deconvolution Wizard:
  • Hybrid AI Filament aware deconvolution is now available.
• (E/P) Quality Control tool:
  • Fixed units of the reported Chromatic Aberration.
• (E/P) Crosstalk & autofluorescence corrector:
  • Add some more tooltips to the histogram.
• (All) File Formats:
  • File Readers:
    • LIF: Fix to get the correct length of XML for reading metadata, this caused the file reader to crash on files from Leica LASX 4.8.
    • OME-TIFF: Improve reading a series of files for specific cases where the files are renamed (for example data written by Luminosa).
  • File Writers:
    • TIFF: fix the TIFF writer not working correctly for saving multi detector images to 16bit.
• (E/P) Main window:
  • Fix Huygens hanging when opening an image with extreme/unlikely sampling ratio's.

24.10.0p1

(5th of December 2024)

• (E/P/L) Main window
  • Fix saving as TIFF not working for selection of multiple images
• (E/P) Crosstalk & autofluorescence corrector:
  • Reduce the number of wizard steps needed for autofluorescence correction.
• (E/P) Deconvolution Express:
  • Hybrid AI Filament aware deconvolution is now available.
  • Fix bug in SNR estimation that could return higher SNR values on images where microscopic parameter templates were loaded and applied.
• (E/P/L) Workflow Processor:
  • Fixed an issue where the analysis task did not work with images with extreme sampling ratios.
  • Fixed an issue where loading some batch templates from older Huygens versions would not load the analysis task correctly.
• (E/P/L) Object Analyzer:
  • Add a new parameter named "iClusCnt", to measure the number of child clusters in the other segmentation group. This parameter has been added to the "Colocalization (intersection)" preset.
• (E/P/L) Microscopic Parameter Window
  • Add new refractive index presets to immersion medium parameter.

24.04 release

• (E/P) Huygens Quality Control option:
  • New option that can be added to your license to automatically investigate the quality of an image.
  • This option can check the microscopic parameters, nyquist rates, SNR estimation, clipping, crosstalk, bleaching.
    • Additionally, "experimental options" are available for checking hot/cold pixels, detector alignment, chromatic aberration, stabilization and PSF shape in an image.
  • Explanations about the issues are given, which helps with identifying and confirming the found issues manually.
  • From the Quality Control option it is easy to correct the issues with restoration options already present included in your license.
• (E/P/L) Huygens Object Analyzer:
  • The UI of the Object Analyzer has been redesigned.
    • Most options are now collected in the left column of the Object Analyzer, distributed over extendable panels.
    • Many more icons have been added to make it easier to navigate the rendering and analysis options.
    • Added a bar with favorites, where you can pin buttons that you often use.
    • Added additional interactive tutorials for multi-channel data, time series and using the ROI.
    • Added color hints to make it easier to see which channel corresponds to which segmentation group.
    • Improved the filter window to make it easier to see which objects will be discarded.
    • Added presets to the filter window.
    • Added a right-click menu to the rendering.
  • Double clicking on a statistics table row now centers the rendering on the corresponding object.
  • Added a new mouse mode called "Select a cluster of objects" for selecting all objects belonging to a cluster.
  • There are now two Object Analyzer license options available to the OA, the Object Analyzer Compact option and the Object Analyzer Advanced option. The former is more economical, the latter offer more features.
• (E/P) Huygens Track Analyzer:
  • Visualize the MIP projection over time.
  • Options to more easily detect and fix possible flaws in the tracks:
    • Find tracks that might need to be connected.
    • Find tracks that might need to be split.
    • Find large objects that were incorrectly detected as two touching objects.
  • It is now possible to add missed objects to tracks.
• (E/P) Huygens Surface Renderer:
  • The UI of the Surface Renderer has been redesigned.
    • Most options are now collected in the right column of the Surface Renderer, distributed over extendable panels.
    • Many more icons have been added to make it easier to navigate the rendering options.
  • Added options for adding and customizing grid rulers.
• (E/P) Huygens Batch Feeder:
  • New options have been added to the Batch Feeder preferences to customize its behavior:
    • The depth of subfolders of the input to recursively search for images can now be changed.
    • It is now possible to preserve the input folder structure for the output folder.
    • It is now possible to automatically run the processing of the Batch Feeder upon startup of the software.
• (P/L) Huygens Python Scripting:
  • Python Scripting is now also available on MacOS
  • NumPy is now included in the Huygens Python interpreter.
• (L) Huygens Cluster Analyzer:
  • Double clicking on a statistics table row now centers the rendering on the corresponding cluster.
  • Improve the filter window: it is now possible to use a filter to keep clusters or discard them and to select a cluster group to apply the filter to.
  • Added the localization density of the cluster convex hull, the h.Density parameter, to the Shrink wrap (convex hull) geometry preset.

Minor Changes

• (E/P/L) Huygens Workflow Processor:
  • Added option to add files in folders recursively.
  • Added option to the saving options task for saving the results in the same folder as the original image.
  • (L) Added the Analysis task to the Workflow Designer.
• (E/P/C) Huygens Stitcher:
  • Improved handling of low values with integer-typed tiles and integer-typed result.
• (E/P) Deconvolution Express:
  • Bleaching correction for time series of all microscope types is now enabled.
• (E/P) Huygens MIP Renderer:
  • Added options for adding and customizing grid rulers.
  • Added some colors from the Matplotlib library.
• (E/P/L) Huygens Object Analyzer:
  • Clicking on a statistics table row corresponding to a cluster now adds all elements of that cluster to the selection.
  • When enabling watershed segmentation, "Use sparse seed" is now enabled as default.
• (E/P) (Twin) Slicer:
  • Option to create an image of the current slice or MIP/Sum projection.
  • Draw circles to measure radii of objects.
  • Added some colors from the Matplotlib library.
• (E/P/L) Rendering in the Object Analyzer, Surface Render, Cluster Analyzer, Colocalization tools:
  • Improved visualization of Surfaces in combination with a MIP in very bright areas.
• (All) File Formats:
  • File Readers:
    • QPTiff: Added support for reading QPTiff's.
    • CZI: Added support for reading .czi files with new Zstandard (zstd) compression.
  • File Writers:
    • OME TIFF: Added support for saving images as pyramid OME-TIFF.
• (L) Workflow Processor:
  • Made the localization 3D calibration parameters editable.
• (E/P/L) Bug Reporter:
  • Made it possible to send information about software issues directly to us when they occur.
  • Made it possible to report an issue via Help->Report issue.
• (E/P/L) Preferences Window:
  • Added a new preference for a directory/folder to hold temporary data.

Bugfixes

• (E/P) Deconvolution Express:
  • Fix a resource leak in deconvolution of time series in cases with spherical aberration where the sub-brick (VarPSF) feature is used.
• (All) File Readers:
  • OBF: Fixed where multi-channel unprocessed MATRIX STED data would be read with wrong dimension orders.
• (E/P/L) Huygens Object Analyzer:
  • Fixed an issue where the "Fill enclosed cavities" option would fail when the number of cavities is very large.

24.04.0p7 (16th of October 2024)

• (E/P/L) Object Analyzer:
  • Fix some parameters not being visible in the Workflow Designer;
  • Fix an issue where some parameters would not get computed for the ROI rows while a coloring is active;
  • (Windows) Fix an issue where when using an imported segmentation, the name of the label image was not shown correctly.
• (E/P/L) Chromatic Aberration Corrector Wizard:
  • Fix issue where wizard crashes when loading a template generated in the Chromatic Aberration Corrector Window.
• (E/P) Track Analyzer:
  • Improve binning in histogram plots showing track statistics.

24.04.0p6 (1st of October 2024)

• (E/P/L) Object Analyzer:
  • Add new parameters named r.ColocV and r.RelColocV for measuring the intersection with the ROI.
  • Fix an issue when loading a template which uses more channels than possible for the loaded image.
  • Fix a regression introduced in 24.04.0p4 that caused analyzing many objects to take more time than needed.
  • The time frame index is now always reported in the table when analyzing time series.
• (E/P/L) Workflow Processor:
  • Fix an error when trying to load a template with an analysis task with a filter step.

24.04.0p5 (26th of August 2024)

• (E/P) Workflow Processor:
  • Fix for lingering .ome extension which was not properly removed when batch processing .ome.tif images.
• (E/P) Huygens Stitcher:
  • Add reading of stage offsets for single-image VSI files, so they can be loaded from the Stitching & Deconvolution Wizard.
  • Fixed an issue that caused a loss of data after converting the stitched result image to smaller datatype in the final stage.
• (All) File Formats:
  • MSR: Fix metadata reading for .msr files written with an updated version of ImSpector.
• (L) Main menu:
  • Fix the Twin Slicer short-cut not being enabled when selecting two images, only for a single image.
  • Fix the Histogram tab for a table failing to compute the histogram for columns with the same value for all localizations.

24.04.0p4 (25th of July 2024)

• (E/P/L) Object Analyzer:
  • Fix an issue causing the "keep object" filter option to not work in some cases.
  • Fix an issue where exporting the rendering would not work when the Workflow Processor, Coloc Analyzer or Cluster Analyzer had been opened before.
  • Fix an issue where analyzing a single object after analyzing clusters could cause errors.
• (E/P) Surface Renderer:
  • Fix an issue where exporting the rendering would not work when the Workflow Processor, Coloc Analyzer or Cluster Analyzer had been opened before.
• (E/P) Workflow Processor:
  • Fix an issue where stitching particular Tiff series could fail.
• (L) Cluster Analyzer:
  • Fix a regression introduced in 24.04.0p0 causing an exported statistics table containing a mistake for the "Applied filters". The reference value or parameters were incorrect (last entry of the line).
• (All) File readers:
  • VSI: Fix a possible crash when reading certain VSI images.
  • VSI: Fix z and t sampling unjustly being reported as read from file in some cases.
  • CZI: Improved file reading speed for very large CZI files
  • CZI: Improved search for Metadata in CZI files where the main "ZISRAWMETADATA" segment could be deleted.
  • ND2: Fix case where (SoRa) Spinning Disk images would not be read in correctly.

24.04.0p3 (2nd of July 2024)

• (E/P/L) Surface Renderer and Object Analyzer:
  • Use global colors by default when this is set in the main window.
• (E/P) Movie Maker:
  • Fix movies using the Surface Renderer failing to save in rare cases.
  • Fix flickering when creating a movie while using the "High Contrast" option in the Surface Renderer
• (E/P) Bleaching Corrector:
  • Fix bleaching templates created in the 24.04 not being loaded in correctly in the Bleaching Corrector.
• (All) File Writers:
  • OME-TIFF:
    • Fix saving an image as pyramid OME-TIFF not working correctly for unsigned 16 bit integer data.

24.04.0p2 (4th of June 2024)

• (L) Cluster Analyzer:
  • Add the "Correlation between channels" preset to analyze the distance of a cluster to its nearest neighbors in the other cluster group.
  • Expanded the parameters on which the color assignment of the cluster can be based on with:
    • The distance to the nearest neighbor in the same/other cluster group;
    • The percentage of voxels of the cluster intersecting with a clusters of the other cluster group.

Bugfixes

• (P/E) Stitching & Deconvolution Wizard:
  • Fix regression introduced in 24.04.0p0a where the tile pattern as read from metadata would be overwritten, even without editing the 'Acquisition pattern' or 'Acquisition overlap'.
• (L) Cluster Analyzer:
  • Fix a regression introduced in 24.04.0p1. The DBSCAN clustering algorithm only worked once each channel (expect the one being currently clustered), has been clustered before, using FOCAL. Only affects multi-channel tables/data.

24.04.0p1 (29th of May 2024)

• (E/P) Image Quality Control Tool:
  • Now keeps track of the correction tools used and reports their usage in subsequent Quality Control reports.
  • Fixed bug with Stabilization Quality Control where some time serie images were always marked as needing a correction.
• (All) GPU processing:
  • Improved the performance of single channel histogram computation on the GPU.
• (All) File Formats:
  • File Readers:
    • OME-TIFF: Fix an issue where Array Detector images saved from Huygens as "One file per detector" could not be read in again correctly.
    • OME-TIFF: Fix an issue where the Array Detector spacing parameter was not read back in correctly for images saved from Huygens.
    • TIFF: Read 16bit signed integer Tiff's into a (16 bit) signed integer Huygens image instead of an unsigned image.
  • File Writers:
    • OME-TIFF: Fix a failure when saving images of less then 256 pixels in X or Y as pyramid OME-TIFF.
• (All) Huygens Everywhere Login Window
  • Made it possible to show/hide the password entry before logging in.
• (L) Table cropper:
  • Fix cropping a table which is already cropped/which itself is output of the table cropper not working.
• (E/P) Stitcher:
  • Improved behavior of overlap and columns entry boxes.
• (E/P) Deconvolution Wizard:
  • Improved behavior of acuity entry box.
• (E/P/L) Object Analyzer:
  • Fixed an issue where it could be impossible to select columns are cells in the table under some circumstances.
  • Fixed the "Add anchors to ROI" option showing an error in some cases.
  • Improved behavior of sorting the table after analyzing a time series.
• (E/P) Surface Renderer:
  • Fixed the rendering being stuck on the first frame for time series.
• (L) Cluster Analyzer:
  • Fix analyzing a channel with DBSCAN setting the cluster of all localizations to 0 in the table for all other channels. Only multi-channel tables are affected. This prevents:
    • Move localizations to main window leading to a table where only the last analyzed channel with DBSCAN has actual clusters not 0.
    • Updating the rendering of a channel not lastly clustered with DBSCAN, by changing the Render mode or FWHM lets all clusters of that channel/Cluster group disappearing from the rendering and analysis.
  • Fix a rare bug that DBSCAN that could change analysis results for touching clusters. DBSCAN with "Ignore border points" is not affected. The Cluster column in the exported localization table is also not affected.

23.10 release

• (E/P/L) Huygens Object Analyzer:
  • (E/P) Track and Analyze objects over time (requires Object Tracking license).
    • It is now possible to link the segmentation of multiple individual frames to each other, allowing measuring how an object changes over time.
    • The linking will also produce tracks, which can also be used in the Track Analyzer.
  • Importing label images for segmentation:
    • Import label images created by various other segmentation software packages (such as for example Cellpose, StarDist).
    • Imported 2D segmentations can also be merged slice-by-slice into a 3D segmentation.
  • Add convex hull (shrink wrap around the object) based analysis:
    • Added options to use the convex hull of a selection of objects/anchors as ROI.
    • Added a new analysis preset for analyzing the geometry of an object's convex hull.
    • Added a new analysis preset for analyzing the distance between objects, based on their convex hulls.
  • Measure surface-to-surface distances between objects and anchors/the ROI.:
    • Added parameters to measure surface-to-surface distances besides surface-to-Center of Mass
  • Extended Watershed segmentation
    • Added additional "Use sparse seed" option for the watershed segmentation that can be used when splitting objects is hard to do with the other options.
  • General performance improvements for the analysis.
  • (E/P) Analysis Workflow Designer:
    • Added Cluster Analysis task to the Analysis workflows.
    • Added task for saving the rendered scene to a JPEG or RGB-TIFF image.
• (E/P) Huygens Workflow Processor:
  • Added Batch Colocalization Analysis.
    • Analyze multiple multi-channel time series images in one go.
    • All channel combinations from the selected channels will be analyzed.
    • Optionally perform background estimation (gaussian minimum, costes method, optimized search) or manually set thresholds in % of the total intensity.
    • The colocalization coefficients table gets exported to a csv file, and a colocalization map can optionally be saved for each channel combination.
    • Note: Region of Interest not yet possible.
  • Added a "convert data type" task for the purpose of minimizing the size of the result image on disk.
    • Before saving, convert the result image to: 32bit float, 16bit (unsigned) integer, or 8bit unsigned byte (might require scaling of intensities to fit).
    • Or choose "Smallest without scaling", which automatically chooses the smallest size where the data fits without scaling.
  • Added flexibility to select which results to save in the "save" task.
    • Option to not save the result image and/or used template.
    • Save additional results: image statistics, Maximum Intensity Projections (along X, Y or Z), and a Thumbnail image of the result.
• (All) File Formats:
  • Added a new file format "Memory Mapped File" with extension (.mmf) as alternative to SWAP
    • Loading Memory Mapped images bypasses the use of system RAM. All image processing with the opened image, will be done directly with the file on disk.
    • This can be used to process images that do not fit in RAM memory. The stitcher uses this format by default when the result image would otherwise not fit.
  • Added support for exporting and reading of PNG images in Huygens.
  • (E/P) Improved support for workflows with Abberior MATRIX STED images.
    • After opening file, the image is split into the raw 23-detector image, and a preview image of the summed central 7 detectors.
    • Improved support for opening these 23-detector images in the Array Detector Quality Control Tool.
• (E/P/L) Huygens Slicer/Twin Slicer
  • New contrast control options:
    • An 'auto' button which cycles through settings of increasing contrast.
    • A slider to edit the contrast range of a specific channel or all channels together.
    • A help button which explains the current contrast settings.
• (E/P) Huygens Sitcher:
  • Memory improvement: Reduced usage of 32-bit float images where possible.
    • Non-deconvolved images can be completely stitched in 16-bit integer datatype, saving memory.
  • Use of the new memory-mapped file (.mmf) file format for temporary and result images when they would not fit in RAM (system) memory.
• (E/P/L) Plot Window:
  • Plots can now be saved as PNG or JPEG images.
• (E/P/L) Huygens Object Tracker:
  • The Tracking algorithm has been improved. This might affect reproducibility of existing tracking templates.
• (L) Cluster Analyzer:
  • Added a new preset to analyze the geometry of the convex hull (shrink wrap) of the clusters.
• (E/P/L) 3D renderers:
  • Added JPEG as export option of current view in MIP and SFP renderer.
• (L) Cropper:
  • Added option to crop Localization Tables.
• (E/P/L) 2D histogram:
  • This window has been updated. It now has various settings and it is resizable.

Minor Changes

• (All) GPU acceleration:
  • Dropped support for graphics cards with a compute capability lower than 5.0 (Cards older than ~2013). See https://svi.nl/gpucards#Huygens_23.10 for a list of affected cards.
  • Dropped support for CUDA Toolkit versions lower than 11. In case you have an older CUDA Toolkit version installed, you will need to update it to a newer version to enable GPU acceleration in Huygens. See https://svi.nl/GpuChecklist for instructions.
• (All) Huygens Everywhere:
  • Rename the term "Group" to "License" to prevent confusion when having to choose between multiple license options.
• (E/P) Huygens Fuser:
  • Update the visualization in the side view when rotating the individual images.
• (E/P/L) Huygens Object Analyzer:
  • Have the conditions rows in the table display more information.
  • Added option to import the ROI from the main window.
  • Add a warning when trying to load an image with default sampling sizes in the Object Analyzer.
  • Useful keyboard shortcuts, like Ctrl-z for undo, now always work when the Object Analyzer is active. Keyboard shortcuts for anchors hav been removed.
  • Improve user interface for the frame slider and the segmentation settings.
  • Improve tutorial text.
  • Improve explanation for the Analyze clusters option.
  • When there is only one ROI component, only print the main ROI row.
• (L) Cluster Analyzer:
  • When selecting a parameter to color on, the coloring is always kept up-to-date, i.e. recompute when the clusters change. Effectively auto-color option is now always on.
  • Added customization of the scale bar.
• (E/P/L) Microscopic Parameters Window:
  • Improve multi photon parameters (photon count) option in the UI. Added a checkbox to indicate that data is acquired with multi-photon excitation.
    When the option is checked, the amount of excitation photons can be entered.
• (E/P/L) Huygens Visualization Tools:
  • Added more customization to the scale bar, including text size.
• (E/P/L) Contrast/LUT editor
  • Improve behavior of dragging control points, especially the end points.

Bugfixes

• (All) Huygens Bleaching Corrector:
  • Fix a rarely occurring bug which only happens for bleaching correction of confocal time series that do not exhibit the typical exponential intensity decay.
    This bug caused non-deterministic selection of one of 2 potential correction strategies.
    • Strategy 1: Correct all frames to match the summed intensity of the primary time frame
    • Strategy 2: Correct all frames to match the averaged intensities of all time frames.
• (All) Microscopic Parameter Window:
  • Fix a bug where manually edited parameters would not count towards accepted or verified status.
• (All) File readers:
  • Ome-Tiff reader:
    • Fix not being able to read ome-tiff files with a custom xml tag starting with Image in the ome-xml meta data, e.g. <ImageVersion .
• (E/P/L) Huygens Object Analyzer:
  • Fix File -> Export Rendering resetting the parameter coloring back to Label.
  • Fix the Object Analyzer being counted too often in the Usage Report.
• (L) Cluster Analyzer:
  • Fix the iso-surface threshold not being correctly taken into account for iso-surface computations. This affects the IsoVol, Surface and RoughSph (VoxArea and RoughRound for 2D data) parameters in the Small clusters geometry preset.
  • Fix visualization bug where exporting the rendering would reset the parameter coloring back to type 'Label'.
• (E/P) Workflow Processor:
  • Fix the "Duplicate" button not duplicating the analysis task.

23.10.0p7 (11th of April 2024)

• (All) File Formats:
  • CZI: Fixed a regression introduced in 23.04 in the CZI reader for Linux when reading CZI files with jpegxr compression.
  • CZI: Fixed an issue where reading Raw Airyscan data from very long file names would not succesfully open in Huygens.
  • CZI: Add improved lightsheet thickness parsing for new czi files from Zeiss Lightsheet Z1 microscopes.
  • OBF: Fixed where multi-channel unprocessed MATRIX STED data would be read with wrong dimension orders.
• (All) Window management:
  • Fix newly opened tools sometimes being placed on wrong monitor in multi-monitor setups.
• (E/P) Workflow Designer:
  • Improve deconvolution workflow for regular Tiff series written by Andor software.
• (E/P) Twin MIP
  • Fix bug where in specific situations the Twin MIP wouldn't start on single channel images.
• (E/P) Deconvolution Express:
  • Fix a resource leak in deconvolution of time series in cases with spherical aberration where the sub-brick (VarPSF) feature is used.

23.10.0p6 (27th of February 2024)

• (All) File Formats:
  • CZI: Fixed a regression introduced in 23.04 in the CZI reader for Linux when reading CZI files with jpegxr compression.
  • TIFF:
    • When writing a tiff that requires scaling, add an option to open the help page on the website.
    • Fix parsing the geometry for plain Tiff's with a resolution unit of inch or centimeter.
  • OME-TIFF: patch reading of files with inconsitent namespace usage in the xml w.r.t. OME attribute and its child attributes.
• (E/P/L) Object Analyzer:
  • Fix a rare bug that could lead to incorrect surface to surface and convex hull distances, specifically the parameters: a.Hull, a.sSurf, r.sSurf.
  • Fix an issue where the segmentation could reset unexpectedly.
• (E/P) Deconvolution Templates:
  • Fixed bug where the Array Detector Reduction Mode was not properly added to GMLE deconvolution task templates.
• (E/P/L) Cropper :
  • Prevent an image with a time dimension of 0 from resulting in a cropped image with a time dimension of 1.

23.10.0p5 (25th of January 2024)

• (E/P) Twin MIP:
  • Fixed that the movie was saved twice when saving a movie from the Twin MIP while linking as "color and channels" or "everything".
• (E/P/L) Slicer:
  • Fixed a bug where "Clone this slicer" did not synchronize the time frame, this also caused bugged behavior when creating a plot in a different time frame than 0.
• (E/P/L) Workflow Processor:
  • Fixed a bug for container images with sub-sub-images, where results could overwrite each other in some situations.
• (P) Operations Window:
  • Fix for the mirror operation to mirror the entire raw Array Detector dataset instead of only the first detector when mirroring in Z and T.
• (E/P) Object Analyzer:
  • Fix an issue causing changes to the current time frame to not be logged to the history is some cases.
  • Fix the ROI cropping option.
• (E/P) Movie Maker:
  • Fix an issue where the rendering could have sudden moves when the zoom is high.

23.10.0p4 (8th of December 2023)

• (All) General:
  • Linux: add support for Ubuntu 23.10.
• (All) File Formats:
  • OME-XML: fix a regression breaking the OME-XML writer since the 23.04 release.
• (E/P) Movie Maker:
  • Fix a regression introduced in 23.04 release, causing the movie maker not to work with the MIP renderer when adding more than 4 key frames.
• (E/P) Stitcher:
  • Fix for loading manual vignetting correction images defined in templates.
  • Added incompatibility warning for the "Automatic" deconvolution algorithm, which cannot be used when stitching.
• (E/P) Deconvolution Express:
  • Changed Acuity sliders responsiveness, new deconvolution previews will now generate after releasing the mouse button.
• (L) PSF Distiller:
  • Fix a regression introduced in 23.04 release, causing an error when distilling a multi-channel PSF from astigmatic 3D SMLM data.
• (E/P/L) MIP/Twin MIP renderer:
  • Changed contrast options to match the new contrast options in the Slicer and Twin Slicer.
  • Improved syncing of color and contrast settings in the Twin MIP renderer.

23.10.0p3 (30th of November 2023)

• (All) File Formats:
  • OBF: Add back the filename in front of the sub-images when loading new Facility Line OBF images which was removed since version 23.10.0p0.
  • Tiff: improve reading pixeldata from 16-bit signed tiffs with intensity offsets as written by ImageJ containing negative values.
• (E/P/L) Microscopic parameter editor
  • Fixed a regression introduced in 23.10.0p0 causing the multi-photon option and photon count only being editable for the first channel.
• (L) Localizer main window:
  • Fixed the Tools-> Join Images main menu bar option not working if there also is a table in the thumbnail selection, regression introduced in 23.04.0p0.
• (L) Cluster Analyzer:
  • Fix the Cluster Analyzer freezing when first selecting another parameter to color on than ClusLabel or RandomClusLabel and then deselecting this cluster pipe, e.g. setting the channel to off.

23.10.0p2 (17th of November 2023)

• (All) Deconvolution
  • Fixed a memory safety error for very large images when finding the optimal bricking layout.
  • Fixed an integer overflow in the PSF generation for very large images with spherical aberration.
• (All) File readers
  • Improved memory safety in the .msr and .obf file reader.
  • Fixed metadata issue for .lif files introduced in 23.04.0p0.
• (E/P) Object Tracker
  • Fixed a regression introduced in 23.10.0p0 where the Tracker would always use the first frame to train on.
• (E/P/L) Object Analyzer
  • Fixed an issue where the "Fill enclosed cavities" option would sometimes not remove all cavities when the GPU was enabled.
  • Fixed an issue where loading a template in the Workflow Designer with two automatically segmented channels would not set the channels correctly.
• (E/P) Object Stabilizer
  • Fixed an issue where stabilizing time series using the Tracker was sometimes disabled.

23.10.0p1 (9th of November 2023)

New features and minor changes

• (E/P/L) Workflow Designer
  • Improve processing speed when selecting multiple image files at once for the "Select Image(s)" task.
• (C/P/L) Huygens Python
  • Command line arguments can now be up to 4096 characters long, up from 128.

Bugfixes

• (All) File Readers
  • OBF: Fix file reader when opening new DyMIN and Rescue STED images written with Abberior Lightbox version 2023.26 and newer.
• (E/P) Deconvolution Wizard & PSF Distiller
  • Fix crash during STED PSF parameter estimation when image name 'psf' is not available.
  • Fix crash that occurred when deconvolving images with very large dimensions (larger than 10,000 x 10,000 pixels).
• (E/P) Object Analyzer
  • In the Workflow Designer, fixed the "Open in Workflow Processor" button not working correctly.
• (C/P/L) Huygens Python
  • Fix Windows not being able to import modules like scipy due to missing python libraries.
  • Fix an issue where image.toNumpy and image.fromNumpy did not work even when numpy was imported.
  • Fix an issue where image.toNumpy and image.fromNumpy would use a wrong dimension ordering.
• (P) Operations Window:
  • Fix a regression introduced in 23.04.0p0 causing the Multi-GPU versions of CMLE, QMLE and GMLE not to work.

23.04 release

• (All) Change in scripting with images/tables:
  • Creating images or tables returns a handle instead of their name.
    • Handles are to be used for Tcl and Python scripting.
    • Previously, the image name served this purpose and images could therefore not be renamed.
  • Rename images or tables without creating copies
    • Right-click the thumbnail and select "Rename Image/Table" or press F2 as a shortcut.
    • Use Tcl scripting with the rename command 'oldName rename newName'
• (P/L) Python Scripting:
  • Updated Python from version 3.7.8 to version 3.11.1
  • Updated the Python image class to be compatible with image handles and image names.
• (E/P) Deconvolution Express:
  • Improved automatic SNR and Acuity estimation. The suggested Acuity can no longer be out of the normal range.
• (E/P/C) Deconvolution algorithms:
  • (CMLE/GMLE) Added a correction to the regularization for images with only one or two z slices.
  • (CMLE) Improved the correction to the regularization for under and oversampled images. This change is almost disabled when acuity is disabled, for better backwards compatibility.
  • Note: Deconvolution templates for shallow and/or very under or oversampled images might need adjustment.
• (E/P) Workflow Processor:
  • Added an "Analyze Objects" task for doing object analysis in batch (see below).
  • Added "Automatic" deconvolution algorithm, which does deconvolution with automatically found settings like in the Decon Express.
  • Added the option to do Crosstalk Correction by using a Crosstalk Correction Template.
• (E/P/C) Batch Object Analysis
  • It is now possible to do Object Analysis in batch by using a new task in the Workflow Processor.
  • (E/P) The Workflow Designer in the Object Analyzer has been improved and modified to support batch processing.
    • The "Time frame and detector" task has been reworked to a "Time series" task. It is now possible to apply parts of a workflow to each time frame in an image. This replaces some old task specific options like "Analyze time series". Support for analyzing raw array detector images has been deprecated.
    • The "Set visualization task" has been deprecated.
    • In the "Basic ROI operations" and "Set anchor" tasks it is now possible to set the segmentation group for some options.
    • The "Advanced ROI operations" task has been expanded with more options.
    • A new "ROI intensity removal" task has been added which can be used to remove intensity from an image by using the ROI.
• (E/P/L) The Object Analyzer
  • Added a tutorial.
  • (E/P) Reported parameters:
    • It is now possible to save and load custom selections of parameters using templates.
  • Added the "HighContrast" parameters to the list of coloring parameters in the visualization tab. This parameter can be used to color objects in such a way nearby objects have contrasting colors.
  • Added mouse modes for drawing selections in regular shapes.
  • Analysis of 2D XY slices will no longer report parameters that are irrelevant or misleading for 2 dimensional images.
  • Added/improved GPU support for merging and removing objects, selecting objects with the lasso tool, and for various analysis operations.
  • Improve selection of objects. It is now possible to select multiple objects by using Ctrl + Left mouse button when in the analyze mouse mode. Selected objects will also be highlighted more clearly.
• (E/P) Crosstalk Corrector:
  • Added support to crosstalk corrector for unprocessed Array Detector images
  • Added Crosstalk Correction Templates.
  • Updated the Mip preview.
• (All) File readers:
  • HDF5 reader:
    • Read Luxendo metadata.
    • Added support for HDF5 images split over multiple files.
• (C) Huygens command line interface (CLI):
  • Start Huygens Core from a command line with paths to a workflow template and an image to apply that workflow template to that image.
    • With this it becomes easy to integrate Huygens deconvolution and processing in your custom workflows.
    • This makes it easy to implement Huygens with a job scheduler (e.g. Slurm).

Minor Changes

• (E/P) Improved raw Array Detector image support:
  • Added detector cropping option to the Cropper.
  • Gallery tool can visualize slices across the detector images.
• (E/P) SFP renderer:
  • Use full resolution while rotating or zooming when this is fast enough.
• (E/P/L) All renderers:
  • Customizable scale bar.
• (E/P/L) Slicer/Twin Slicer/MIP renderers
  • Overlay hue bar that shows the look-up table of the image.
• (E/P) PSF Distiller:
  • Made the STED Parameter estimation optional. You can now directly export your distilled STED PSF as is.
  • Lowered the allowed diameter for STED beads from a minimum of 25nm to 20nm to account for STED GATTA-Beads of 23nm.
  • Improved suggested SNR value and allowed different SNR values for different channels when distilling multiple channels from one image.
• (All) File readers:
  • Abberior Msr/Obf:
    • Improved reading speed of chunked obf files containing large tile series and/or time series.
    • Fixed reading of the angle for rotated tile acquisitions in both Facility Line and STEDYCON files.
  • Tiff reader:
    • Added support for tiled tiffs with 8/16 bit (unsigned) integer and 32 bit (unsigned) integer/float datatypes.
    • Partial support added for 32 bit integer tiffs. These will be read in and converted to (32 bit) float images.
  • Ome-Tiff reader:
    • Improved reading in the data of a single file from a file series for special cases, for example files written by VisiView.
    • Improved attaching the channel meta data when loading a subset of the channels of the full image.
• (All) File writers:
  • Ome-Tiff writer:
    • Save all Huygens Microscopic parameters not fitting in the OME schema to a custom SVI StructuredAnnotation.
    • All Huygens Microscopic parameters are now saved when using the OME-TIFF format, including STED, SPIM and Array Detector parameters and the parameter reliability states.
• (E/P/L) Export of rendering:
  • Added the option to export to the Surface Renderer and Object Analyzer.
  • Added the option to export without border at original size in the Slicers.
• (L) Cluster Analyzer:
  • Analysis of 2D tables will no longer report parameters that are irrelevant or misleading for 2 dimensional data and now contains relevant roundness measures for 2D data.
  • New coloring options: it is now possible to color the clusters based on some of their properties. For instance clusters with the same parent can be given the same color.
  • Add the "HighContrast" parameters to the list of coloring parameters in the visualization tab. This parameter can be used to color objects in such a way nearby clusters have contrasting colors.
• (E/P/L) Preferences:
  • (P/L) Add setting for the prefered scripting shell (Python or Tcl).
• (E/P/L) License Window:
  • Improve description when adding a license that does not work for the open product.

Bugfixes

• (E/P) Deconvolution Express:
  • Fixed a bug when not supersampling all but at least one Array Detector channel.
• (E/P/L) Workflow Processor:
  • Fixed small bugs that could happen when opening series files.
  • (E/P) Fixed a bug when not supersampling all but at least one Array Detector channel.
• (E/P/L) Twin Slicer:
  • Fixed an issue where the right viewer of the Twin Slicer would not use the correct z-slice when the viewed images have different z-sampling.
• (E/P/L) The Object Analyzer
  • Fixed a rare issue where the analysis would not continue correctly when pressing the stop button during analyze all.
  • Fixed an issue where parameters depending on the principal axes were not computed correctly for objects with negative principal components.
• (E/P/L) The Object Tracker
  • Fixed an issue where the training could fail when two channels are very similar.
• (All) File readers:
  • Olympus VSI: fixed crash when reading a file with a large number of acquisition markers.
• (L) Cluster Analyzer:
  • Fixed an issue where parameters depending on the principal axes were not computed correctly for objects with negative principal components.

23.04.0p7 (18th of October 2023)

• (E/P/L) Thumbnails:
  • Fixed thumbnail brightness inconsistencies when switching between 2D and 3D modes.
• (E/P) Workflow Processor:
  • Fixed the issue where loading custom darkframe and flatfield images in the Stitching task was not possible.
• (C) SNR utilities for the HRM:
  • Fixed regression introduced in 23.04.0p0 for the "Legacy" SNR estimation in the HRM that caused it to never work.
  • Fixed bug for the "Auto" SNR estimation in the HRM where the shown previews were not correct when an intermediate step for SNR estimation failed.
• (E/P) Movie maker:
  • Fixed issue with downsampling that resulted in an error when using the Movie Maker with the Surface renderer.

23.04.0p6 (14th of September 2023)

• (All) File readers:
  • OME-TIFF: Fixed regression introduced in 22.10 causing for some files to read in only the first slice instead of the full z-stack, for example some ImSpector exported data.
  • CZI:
    • Fixed an issue where images with invalid wavelength values could not be opened.
    • Fixed an issue where backprojected pinhole values where not estimated correctly when only a few channels have metadata for them.
    • When the microscope type cannot be determined from the metadata, use "confocal" as default.
• (E/P/L) Object Analyzer:
  • Fixed an error when hovering over an object after sorting the table.
• (E/P/L) Hot & cold pixel remover in Workflow Processor:
  • Fixed a bug where for images with a particular dimension setup a valid mask image would be rejected as having the wrong dimensions.
• (E/P) Interactive Fuser:
  • Fix regression introduced in 23.04.0p0 where image data could not be processed in the fusion steps.
    *Applies only to data where all rotational views are opened from a single container image file format like .CZI or .LIF files.
• (E/P) Array Detector Quality Control Tool:
  • Change default value of intensity coloring to scale with respect to the detector with maximum intensity instead of central detector.

23.04.0p5 (24th of August 2023)

• (E/P) Array Detector Quality Control Tool:
  • Add support for Airyscan 2 images;
  • No longer show the "Shift" tab for preprocessed detector models for which shift computations are not possible.
• (L) Cluster Analyzer:
  • Fix the auto color option not working correctly when enabling this option with an out-dated clustering, i.e. changing cluster parameters without pressing Cluster & Render and then enabling the auto-color option in the Visualization tab.
• (L) Localizer:
  • Improve the localization of rare particles where the initial guess has a negative intensity after background subtraction. This might add localizations to the final result as such these rare particles are no longer directly discarded. The values of the other localizations are unaffected.
• (E/P) Object Stabilizer:
  • Use a more notable button for entering the wizard.
• (E/P/L) User Interface:
  • Improve the contrast of the highlighted text for some entry boxes.

23.04.0p4 (25th of July 2023)

New features and minor changes

• (E/P/L) Object Analyzer (Basic):
  • Add convex hull based analysis.
    • Added option to set the ROI to the convex hull of a selection of objects.
    • Added two new analysis presets: for analyzing the geometry of the convex hull of an object and for distance between objects based on their convex hulls.
    • On-the-fly visualization of the convex hull when hovering over a convex hull related parameter in the statistics table.
  • (E/P) Improve settings in the segmentation task of the Analysis Workflow Designer
    • Separate the entries for the threshold, seed, and sigma when doing automatic estimation, instead of one setting that controls all.
  • (E/P) Add option to load a different ROI for each input image in to the "Load ROI from file" option.
  • Extend file formats used to read and write ROI's from just hdf5 to hdf5, ics, ome-tiff and tiff.
• (All) Hot & Cold Pixel Corrector:
  • Changed detected hot/cold pixel overlay to be drawn on the result on the right, for easier comparison with the original hot pixels on the original on the left.
  • Overlay visualization option is now a checkbox that either shows or hides the Hot/Cold Pixel Mask on top of the result image.
• (All) File readers:
  • IMS: The Brightfield microscope type is now read from new Imaris files.
  • MSR: Parse objective information for imspector .msr files.
• (All) Rename tool:
  • Improved scalability of rename window for larger image names.
• (E/P) File series tool:
  • Allow users to open tiles from a file series in the Huygens main window instead of forcing them directly to the Stitcher.
• (C) Command line interface:
  • Allow setting which GPU device to use for a template by using the -gpuDevice option on the command line.
• (E/P) Colocalization Analyzer:
  • Extend file formats used to read and write ROI's from just hdf5 to hdf5, ics, ome-tiff and tiff.

Bugfixes

• (E/P) QMLE Deconvolution:
  • Fix issue where early stop requests during QMLE deconvolution would not result in the end of the deconvolution run.
• (All) File readers:
  • OBF: Fix for Facility Line and Infinity Line .obf files only showing separate channels due to new version number schema in OME-XML metadata.
  • TIFF: Fix a rare issue where only the first slice was loaded on Linux.
• (E/P/L) Workflow Designer:
  • Fixed a bug when using the fileseries tool with the ignore or "numerical" setting.
  • Fixed a bug for stitching templates where the channels used for stitching would unintentionally reset.
  • Fixed a bug where loading a template with the "Load ROI from file" option would give an error.
  • Fixed a bug where loading a decon template with a single deconvolution task set all 32 channels to verified.
• (E/P) Deconvolution Wizard:
  • Fixed a crash when processing a multi-photon image with negative values.
• (E/P) Stitching Wizard:
  • Fixed a bug where templates were not accepted due to a non-existing mismatch in dimensions.
• (E/P) Colocalization Analyzer:
  • Fixed an issue where the Colocalization Analyzer Compact & Advanced tools could not start with RBNCC options enabled.
• (L) Cluster Analyzer:
  • Fix an issue where clustering the same channel with different settings in both pipes, could go wrong in a rare case.
    • When first clustering the channel in pipe A, then the clustering (the same) channel in pipe B and finally the visualization settings Render mode and/or FWHM of pipe A are changed, pipe A copied the clustering of pipe B in the rendering and analysis. Here clustering means pushing the Cluster & Render button.
• (L) Localizer 2D/3D:
  • Fix a rare crash during the localization on Linux.

23.04.0p3 (3rd of July 2023)

• (All) Deconvolution:
  • Fixed regression from 23.04.0p0 resulting in sub-optimal results for densly (over)sampled confocal images at larger iteration counts.
  • Improved Signal to Noise Ratio estimation for non-descanned detector Multi-photon images.
• (E/P) Deconvolution Wizard/Express:
  • Added an extra check for NA and refractive indices to prevent potential crashes in the Deconvolution Wizard and Deconvolution Express.
• (All) Workflow Processor:
  • Print image names instead of image handles in the progress report of the workflow processor.
• (All) File reader:
  • All: Fixed regression from 23.04.0p0 resulting in "File does not exist" errors when trying to read files that contain consecutive spaces in the filename.
  • LIF: Improved reading of the emission wavelength for widefield .lif images.
  • MSR/OBF: Add imspector XML metadata parsing for Expert Line .msr files.
  • TIFF: Add better support for reading pixeldata from 16-bit signed tiffs with intensity offsets as written by ImageJ.
• (C) Command line interface:
  • Fix issue where the default value for the -imgOpen CLI option caused a template to fail. (This affected HRM.)
• (L) Object Analyzer Basic:
  • Fixed Cluster Analysis not finding any clusters.
  • Fixed some coloring parameters not working.
• (All) GPU support
  • Fixed regression from 23.04.0p0 where Cuda Toolkit version 11.6 could not be used with Huygens 23.04.
• (P/E) Chromatic Aberration Correction Wizard:
  • Fix for the error messages "Value for 'threshG' is below range: resetting to 0.000000" for integer-typed images with very low values.

23.04.0p2 (2nd of June 2023)

• (C) Fix locale issues for HRM and HuCore users
  • Prevent problems that could arise from the potential use of the comma (,) as decimal separators instead of period (.).
• (All) File reader:
  • MSR/OBF: Fix issue where images would only open up as separate channels. (Affected versions were 23.04.0p0 and 23.04.0p1)

23.04.0p1 (1st of June 2023)

• (All) File reader:
  • Olympus VSI: Prevented crash when trying to open an invalid VSI file.
  • OME-TIFF: Fixed regression from 23.04.0p0 introducing a potential memory leak.
• (E/P) Workflow Processor:
  • Ensured the correct names are used when saving series images.
  • Fixed getting a lot of warnings about Chromatic Shift Correction in some situations where it was not used.
  • Fixed error when trying to execute an analysis template that shifts the ROI.
• (P) Operations Window:
  • Fixed issue where results of operations were not shown when using images a, b, c or psf as output.
• (C) Command line interface:
  • Prevented problems when using the -series option in HuCore intended as argument for a script.

22.10 release

• (L) Cluster Analyzer: new tool in the Huygens Localizer for cluster analysis of localizations:
  • Cluster the localizations in 2D or 3D using the FOCAL or DBSCAN algorithms.
  • High quality iso-surface rendering of clusters using ray tracing.
  • Measurements for volume, localization density, width, length and more of the clusters.
  • MIP rendering to use a specific channel as a reference for determining the optimal cluster parameters.
  • In-tool tutorial to get started and familiarize yourself with the main features.
  • Direct link between the rendered scene and cluster statistics table: select clusters to highlight them in both.
  • Extensive filtering options and option to export the cluster statistics to spreadsheets (.txt or .csv) or Matlab (.m).
• (All) File readers:
  • Olympus OIR reader:
    • Full support for reading Olympus OIR files on all platforms: Windows, Linux and Mac(x86)*.
• (All) File writers:
  • OME-TIFF:
    • Added an OME-TIFF writer to Huygens.
    • Save 5D OME-TIFF files and support writing multi-detector images using file series.
• (E/P/L) Object Analyzer:
  • Add reported parameter for measuring the average intensity of an object.
  • Expand the list of parameters that can be used for coloring.
  • (E/P) Add an "export segmentation" button.
  • Add rows to the table for each connected component of the ROI.
• (E/P/L) Microscopic Parameters Window:
  • Improve clarity of the parameter status symbols:
    • Verified parameters are now marked with a green checkmark.
    • Parameters that are read from file are now marked with a green dot.
• (All) Mac M1 installer:
  • Full support for the Huygens Software suite, optimized for ARM-based M1 chips.
• (C/E/P) Deconvolution:
  • Specific deconvolution for SoRa systems, included in the Spinning Disk option.
  • Add new microscope type for VisiTech iSIM data.
• (E/P) Array Detector Quality Control:
  • Add a new tool for analyzing individual detector intensities and shifts for array detector images.
• (C/P/L) Python:
  • Add functions to export Huygens image data to Python lists and vice versa.
• (E/P/L) Help:
  • Help functions that can be found in the Huygens Core manual is now automatically opened in a Huygens Core manual.
• (E/P) Workflow Processor:
  • Added support for batch stitching based on XML files with offsets.
• (E/P/L) MIP rendering:
  • Improve accuracy of the rendering, especially when zoomed in.

* With the exception of ARM M1-based Macs

Minor changes

• (E/P) Workflow Processor
  • Add option to save z mip of the image.
• (All) File readers:
  • Tiff reader:
    • Improve support for tiff files written by imageJ, especially for large files (BigTiff).
    • Add support for reading jpeg encoded tiff files on Windows.
    • Add support for reading deflate compressed tiff files on Windows.
  • OME-TIFF reader:
    • Improved reading of different OME-TIFF file configurations, including files written by Slidebook.
    • Improved reading of metadata.
  • Olympus VSI:
    • Improved reading of metadata.
  • Nikon ND2:
    • Improved feedback after failing to read a file.
    • Improved reading of metadata.
• (All) File writers:
  • Tiff: Add support for writing multi-detector images.
• (E/P/L) User interface:
  • Add sliders to make it easier to navigate through channels, time frames and detectors in the histogram tab in the main window.
  • Added image dimension in the sub-image selection window.
• (E/P/L) Cropper:
  • Improve automatic cropping for array detector images.
• (E/P/L) Chromatic Aberration Corrector:
  • Automatically choose the initial setting for the reference channel.

• Huygens Nyquist Calculator (on svi.nl)
  • Added the new Sora and VT-iSIM microscope types.
  • Added Zeiss Airyscan 2 Sheppard Rings detector model for array detector microscopes.
  • Sanitize and warn for lens immersion refractive index and numerical aperature mismatches.
  • Warn for an invalid combination of wavelengths and excitation photon count.

Bugfixes

• (E/P/L) Microscopic Parameters Window:
  • (Windows) Fix some options not being visible.
• (All) Gpu processing:
  • Fix an issue where GPU processing would not get enabled when switching from a license that does not allow GPU processing to one that does.
• (E/P) (Twin) Mip Renderer:
  • Fix an issue where the depth rendering would not work for images with more than 4 channels.
• (E/P/L) Preferences
  • Fix an issue where thread restrictions were not applied correctly in some cases.
• (All) File readers:
  • OME-XML reader:
    • Fix reading in files upside-down, i.e. with an inverted Y-axis.
    • Enable reading OME-XML files written in the the 2016_06 schema.
  • OME-TIFF reader:
    • Fix the -series auto option of img_open not recognizing a series for files with .ome.tif(f) extension.
  • Abberior OBF:
    • Fix regression where some older obf files with compression were not read.
• (All) File Writers:
  • OME-XML writer:
    • Fixed issue where files were saved upside-down, i.e. with an inverted Y-axis.
• (E/P) Bleaching Corrector:
  • Fix an issue where access was wrongly blocked when only multi-photon microscopes were licensed.
• (L) Table Export window:
  • The 'The name of the table to create' entry now actually becomes the name of the opened table.

22.10.0p6 (12th of April 2023)

• (E/P) Stitching & Deconvolution Wizard
  • Fix reading of angle for rotated OBF tile series in the stitcher.
• (E/P) Deconvolution Wizard
  • Fix reduction mode setting for multichannel array detector images.
• (P) FWHM estimator:
  • Fix a rare crash that could occur in the FWHM estimator.
• (P) Image Convert tool
  • Fix an XY(ChZ) -> XYZCh conversion unintended changing the coverslip position.

22.10.0p5 (1st of March 2023)

• (All) File reader:
  • LIF: Fix only reading in the first sub image for FLIM Tau STED data.
  • OBF/MSR: Fix memory leak that occurred for tiled datasets when parsing OME-XML metadata in OBF files.
  • OME-TIFF: Fix the offset of a multi-file series for files exported by VisiView.
  • OME-TIFF: Fix an issue where only a single z-slice was read in from a z-stack for files exported by ImSpector.
  • OME-TIFF: Fix for rare case where the ome-tiff reader could hang.
  • OME: Fix memory leak that occurred when reading in OME-TIFF or OME-XML files.
  • (C) VSI / ND2: improve reading metadata for spinning disk images.
• (L) Cluster Analyzer:
  • Fix the threshold (slider) not correctly initializing to 0.5 for all channels except the first one.
  • Fix the average intensity parameter not being reported.
• (E/P) Decon Wizard:
  • Fix an issue where the iteration count used for QMLE was not updated properly when editing the acuity or SNR.
• (E/P/L) Object Analyzer:
  • Fix an issue causing distance to surface computions to take much longer than needed.
  • Fix an issue where formerly removed objects could not be highlighted anymore after reloading the data.

22.10.0p4 (7th of February 2023)

• (All) File writer:
  • TIFF: fixed an issue where multi-directory tiffs/tiffs contain all z-slices in a single file could overwrite existing files without a warning.
  • TIFF: no longer remove the last number in the filename when saving a tiff series, if the number is not clearly a slice, time frame, channel or detector counter.
• (E/P/L) Object Analyzer:
  • Fix an error when selecting all objects as anchors.
  • Fix an error when changing the threshold value in the MIP segmentation group.
• (L) Cluster Analyzer:
  • Fix distance configured to be reported on-screen not being plotted for 2D data.
• (All) Deconvolution:
  • GMLE: fixed a resource leak that could cause deconvolution to fail with an error: "Variable overflow detected during execution"
• MacOS Ventura:
  • (E/P/L) The release of macOS Ventura introduced a regression that caused applications handled by XQuartz (like Huygens) to get unexpectedly minimized in some cases. This patch adds some workarounds to mitigate this, but some issues might persist.

22.10.0p3 (4th of January 2023)

• (All) File writer:
  • OME-TIFF: fix regression, since 22.10.0p1, writing the companion.ome file at the wrong location.
  • OME-TIFF: fix issue with writing (and reading) multi-detector images containing multiple slices/frames or/and channels.
• (All) File reader:
  • ND2: fixed an issue where for some SoRa images the pinhole diameter was not read correctly.
• MacOS:
  • (E/P/L) Extend the fix for font related crashes that was first deployed in 22.10.0p2. In particular, these type of crashes should now also be fixed on macOS Ventura.

22.10.0p2 (13th of December 2022)

• (All) License manager:
  • Fix regression where errors would not be displayed when adding a wrong license to the license manager.
• (All) GPU Processing:
  • Improve description of steps to take when CUDA Toolkit is not found.
• (E/P/L) User Interface:
  • Fix a regression where some help links would lead to https://svi.nl/HuygensDocumentation instead of their intended target since version 22.10.
• (E/P/L) Object Analyzer:
  • Fix an issue where pressing "Reload original data" would not reinstate objects in all time frames and/or detectors.
• (E/P) Mip Renderer:
  • Fix an issue where the Mip Renderer could crash when rendering a very large image in High Quality mode.
• MacOS:
  • (E/P/L) Fix an issue where Huygens could crash when a specific font library would fail.

22.10.0p1 (30th of November 2022)

• (All) File reader:
  • CZI: fix crash on Windows when reading JPEG-XR compressed data.
  • OME-XML: fix a regression breaking the OME-XML reader since the 22.10 release.
• (All) File writer:
  • OME-TIFF: fix OME-TIFF writer not correctly handling file paths longer than 128 characters.
  • OME-XML: fix a regression breaking the OME-XML writer since the 22.10 release.
• (All) GPU Processing:
  • Fix Huygens crashing when loading the CUDA library fails in an early stage.
• (E/P) Decon Express:
  • Fix an issue where the result image could have incorrect scaling when operating under low memory conditions.
• (E/P/L) Object Analyzer:
  • Fix an issue where some operations (such as deselecting all anchors) were not applied to all time frames and/or detectors.
• (E/P/L) User interface:
  • Improvements for the user interface scaling that can be set in the preferences.
• (E/P) Ortho Slicer:
  • Fix a regression where xz- and yz-slicers were initialized at the wrong position.

22.04 release

• (E/P/L) Object Analyzer: Full version available in Professional and Essential, basic version available in Localizer
  • New coloring options: it is now possible to color the objects based on some of their properties. For instance objects with the same parent can be given the same color.
  • Added tools for cluster analysis. In the Object Analyzer it is now possible to cluster objects with the DBSCAN algorithm. The resulting clustering can be visualized in the rendering, and the cluster ID of each object will be saved in the table. Furthermore, some properties of the clusters themselves will also be reported.
  • The new reported parameter ObjectCnt can be used to count the number of objects inside the ROI or in a cluster.
  • Added the "Quick analysis" preset that only reports the basic parameters.
  • The watershed segmentation algorithm will now create larger segments overall, and a new parameter was added to better control how much objects will be split up by the watershed algorithm.
  • The table now has a "customize table" button where one can control which rows need to be displayed.
  • The Object Analyzer now remembers which objects were merged or removed after switching channels, time frames or detectors.
  • Workflow Designer (E/P): add support for the newly added segmentation and coloring options.
• (E/P/L) Look-Up Table (LUT) Editor:
  • Addition of a new look-up table (LUT) editor to the (Twin) Slicer and (Twin) MIP renderer.
  • Color images using custom-made look-up tables mapping image intensities to colors.
  • Use the LUT tab in renderers to load, view and edit Huygens CSV-based LUTs and .lut files.
  • Define look-up tables for the channels of your image and interactively view the effects in the renderers.
  • Adjust your LUT with ease using the graph or wedge-based representations.
  • Add smooth color transitions (i.e. color gradients) to specific selections of look-up table elements.
• (E/P/L) Object Tracker & Track Analyzer:
  • Add spiderplot in Positions tab to see all object's paths with respect to their origin.

Minor changes

• (All) File readers:
  • OME-TIFF: Improve reading files using a header only in the first .ome.tiff or companion file to store the OME-XML metadata.
• (P) File writers:
  • TIFF: when using the contrast stretch mode the scaling factors are now reported in the task report.
• (All) GPU Processing:
  • Added GPU support for a number of 2D image rendering commands.
• (E/P) Deconvolution Express and the Deconvolution Wizard:
  • Improved interactivity.
• (All) Deconvolution templates:
  • Added the possibility to "Remove" a channel instead of skipping it if you don't want to process it.
• (E/P/L) (Twin) Slicer and (Twin) MIP renderer:
  • When exporting an image, it is now possible to set the dimensions of the exported image.
• (E/P) Surface Renderer and (E/P/L) Object Analyzer:
  • The minimum size of an object can now be specified in either micron² or micron³ or in the number of voxels.
  • It is now possible to apply a Gaussian filter (smoothing) before segmenting the image (previously this was only possible when watershed segmentation was used).
• (E/P/L) License Window:
  • Added an overview with the currently activated license options, including links to relevant web pages.

Bugfixes

• (E/P) Deconvolution Express and the Deconvolution Wizard:
  • Fix an issue with the deconvolution preview for superY and superXY deconvolution with Airyscan images.
• (E/P/L) Object Analyzer:
  • Fixed an issue where sorting the table columns would not work in some cases.
• (E/P) Object Stabilizer:
  • Improved handling of time series for the light-sheet deskewing option
• (P) Operations Window::
  • Fixed the "Analysis -> Plot line profile" operation.
• (E/P/L) User Interface:
  • On Windows show a separator icon to indicate the possiblity of dragging to change the size of a window.
• (E/P) Interactive Fuser & Decon:
  • Fix incorrect memory estimation on opening a file when not all sub-images were selected for fusion, resulting in a "The file is too big to load" error.

22.04.0p7 (19th of October 2022)

• (All) File reader:
  • OME-TIFF: fix some .companion.ome files not being read correctly on Windows.
  • CZI: improve estimation of backprojected pinhole sizes.
  • VSI: Fix a rare issue where the image data would appear slanted when opened in Huygens.
• (E/P) Deconvolution Express:
  • Fix an issue where access was wrongly blocked when only multi-photon microscopes were licensed.
• (E/P/L) Object Analyzer (Basic):
  • Fix setting the parameters to be displayed on scene when loading a predefined preset from the preferences.
• (E/P/L) User interface:
  • Various improvements for the user interface scaling that can be set in the preferences.

22.04.0p6 (20th of September 2022)

• (All) Deconvolution, Parameter Editor and related Huygens Tcl commands:
  • Add new microscope type VT-iSIM for Visitech iSIM data.
• (All) File reader:
  • CZI: fix an issue where pinhole sizes were estimated incorrectly for some multi-channel images.
• (E/P) Deconvolution Wizard.
  • Fix a rare crash during deconvolution of brightfield images.
• (E/P/L) Cropper:
  • Fix an issue where the cropper could get stuck when the GUI scaling was set to a value slightly higher than 1.
• (L) Table Export window:
  • Fix an issue where selecting one of "Apply a 1/2 pixel shift to the XY origin" and "Flip the Y axis" always applied both.
• (L) Main menu:
  • Fix the option to shift an image in 3D under Tools->Shift Image.

22.04.0p5 (23rd of August 2022)

• (E/P/L) Object Analyzer (Basic):
  • Fixed an issue where the coloring based on the analysis parameters resets when changing the transparency depth.
• (E/P) Stitcher:
  • Fix for errors that could happen when loading multiple sets of tiles from a single container file.
• (E/P) Workflow processor:
  • Fixed an issue with the thumbnail previews on Windows not showing up.
• (All) GPU Processing:
  • Allow the GeForce RTX 3090 Ti card to be used with the large GPU license option.
• (All) Windows:
  • Fix for issue that showed a warning* that would shut down Huygens if closed.
    *OMP: Warning #... Cannot not determine machine load balance - Using KMP_DYNAMIC_MODE...

22.04.0p4 (3rd of August 2022)

• (E/P) Deconvolution Wizard:
  • Fix a rare crash of the Wizard in the automatic background estimation stage.
  • Fix a bug where the QMLE algorithm for widefield and spim images would always deconvolve using the default settings.
• (E/P) Movie Maker:
  • Fix an error pop-up when switching from the Surface Renderer to another renderer.
  • Fix an issue where the Movie Maker could no longer start a new renderer after the launch of one of them was cancelled.
• (E/P/L) Object Analyzer (Basic):
  • Fixed an issue where statistics were not reported for some objects when both the Gaussian Filter as well as the Minimum Object Size option were used.
• (E/P/L) User Interface:
  • Fix DPI scaling being accidentally applied twice on startup.
  • Limit resizing of the Histogram Tab so that it cannot be hidden, or completely overlap the thumbnail panel.
• (E/P/L) Workflow Processor:
  • Fix an error with thumbnail creation that could occur when there was a space in the path to the output directory.
• (All) OME-TIFF reader:
  • Improve reading the object settings form SlideBook images.
• (All) OBF/MSR reader:
  • For STED channels, the STED mode for Abberior files is now initialized to STEDYCON (Facility/Expert).
• (E/P/L) MIP Renderings:
  • Introduction of a hot pixel corrected display range.

22.04.0p3 (5th of July 2022)

• (E/P) Deconvolution Wizard:
  • Fix a regression introduced in the previous patch (22.04.0p2) where the Deconvolution Wizard would crash after opening the Deconvolution Preview.
• (All) GPU Processing:
  • Allow the GeForce RTX 3080 12GB card to be used with the large GPU license option.

22.04.0p2 (29th of June 2022)

• (E/P) Decon Express:
  • Fix an issue where the "Adjust acuity" stage would not start for some images.
• (E/P) Deconvolution Wizard:
  • Remove unnecessary warning about the backprojected pinhole being too large for array detector images.
• (E/P/L) Hot & Cold pixel remover:
  • Fix an issue where the display option to show both the image as well as the hot/cold pixels did not work since the 22.04 release.
• (E/P/L) Workflow Processor:
  • Fix a rare issue where images containing identically named subimages were not opened correctly.
• (All) File Readers:
  • Metamorph STK: Sampling distances and the emission wavelength are now read from file.
  • Metamorph ND 2.0: Z sampling is now always read from file.
  • OBF Facility Line: Fix issue where reading tiles ended up in detector-dimension due to unexpected DimensionOrder XYZCT.
• (E/P/L) Look-Up Table (LUT) Editor:
  • UI update for more ergonomic use.
  • LUTs are no longer forced to start at black.
  • LUT changes now always apply to the currently edited channel, with the option of applying to all other channels.
  • Various bugfixes.

22.04.0p1 (2th of June 2022)

• (All) Czi file reader:
  • Fix regression introduced in 21.10.1 where the backprojected pinhole size was not computed correctly when no physical pinhole size was present in the metadata.
• (E/P) Surface Renderer:
  • Fix regression introduced in 22.04 where the slicer option would only display channel 0.
• (E/P) Deconvolution Wizard:
  • Fix regression introduced in 21.10.1 where a measured PSF would not be saved properly in templates.
• (E/P) Stitcher:
  • Fix regression introduced in 21.10.1 causing problems with using .xml files for stitching.
  • Fix regression introduced in 21.10.1 causing deconvolution always being skipped.
• (L) Tables:
  • Fix an issue where the values of the FWHM-X(FWHM-Y) where stored in the FWHM-Y(FWHM-X) column. This does not change the z-position of the localizations for 3D SMLM.

21.10 release

Object Analyzer: Full version available in Professional and Essential, basic version available in Localizer

• Add the possibility to use the lasso tool to merge objects.
• Add two new reported parameters for counting objects that are contained in an objects in the other segmentation group. The parameter iParent reports the label a child object is contained in, the parameter iChiCnt reports the number of child objects contained in the parent object. These two new parameters are included in the "Colocalization (intersection)" experiment preset.
• Improve performance of the analysis itself, especially for parameters related to distance to surface (up to 45 times faster) and parameters related to nearest neighbors (up to 6 times faster).
• Add buttons to the main Object Analyzer window for exporting the ROI to the main menu and for redoing actions.
• Improve formatting and readability of the result table.
• Improve handling of very large objects.
• (E/P) The "PS" segmentation mode has been removed.
• For watershed segmentation, the initial sigma for the gaussian filter is now estimated based on image properties.
• (E/P) In the Workflow Designer in the Object Analyzer, add more options for modifying the ROI.
• (L) the Object Analyzer Basic now contains a second segmentation group for analyzing two channels at once.

Workflow Processor (E/P/L)

• (E/P) It is now possible to do Stitching with the Workflow Processor.
• (E/P) Create and edit Stitching templates in the Workflow Designer for the Workflow Processor.
• Customize which templates are shown in the Workflow list in the Workflow Processor.
• Improvements in the user interface of the Workflow Designer.
• The time out for each Workflow is now more easy to change, an option for time out was added to the Workflow Processor menu.
• The saving file format is now a preference and will be remembered between instances of Huygens.

Image Stitcher & Deconvolution (E/P)

• It is now possible to create and use Stitching templates.

MIP Renderer (E/P/L)

• (E/P) There now is a Twin MIP renderer to quickly compare two 3D volumes.
• More advanced contrast settings like in the (Twin) Slicer, this makes it a lot more versatile.
• Improvements in the backend to facilitate these changes.

File Readers (All)

• Support for the Imaris 5.5 HDF5 file format.

Minor changes

• (E/P/L) Renderers:
  • Changed scroll-direction to zoom in and out in all the renderers to better fit zooming conventions.
• (E/P/L) (Twin) MIP Renderer, Slicers, Render Panel and Thumbnails:
  • Addition of a "heat map" color mode.
• (All) Nikon ND2 files:
  • On Windows and Linux the spinning disk metadata for most microscopes is now read from file.
• (All) Image metadata:
  • New Channel Label can now be specified for every channel in an image.
  • Channel labels can be modified in the Microscopic Parameters window.
  • Channel labels are displayed in the channel selector widget.
  • Read and write support for channel labels for ICS and Huygens HDF5 files.
  • Channel labels are now read from Nikon ND2 and Imaris 5.5 HDF5 files.
• (E/P/L) Track analyzer:
  • Plots under the intensity tab now show all tracked channels.
• (All) GPU processing:
  • For Windows and Linux, centralize the NVIDIA cache in the Huygens installation folder. This fixes potential delays when launching Huygens.
• (E/P/L) GUI Scaling:
  • Improve GUI scaling for various dialogs.

Bug Fixes

• (E/P) Surfacer Renderer:
  • Fix rendering sometimes becoming unresponsive when using the high quality MIP.
• (E/P/L) Object Analyzer:
  • Fix an issue with growing the ROI in the Z dimension.
• (E/P) Deconvolution Wizard:
  • Fix the Decon Preview using some data from channel 0 instead of the selected channel.
• (E/P) Colocalization Analyzer Advanced:
  • Fix an issue where Huygens could freeze after computing the colocalization coefficient while the Colocalization Analyzer was being displayed on a low resolution screen.
• (E/P) Deconvolution Express:
  • Fix the window not being closable after the deconvolution encounters an error.
  • (E) Fix an issue where in some cases, when trying to open the Deconvolution Express, the Deconvolution wizard would open instead.
• (E/P) Stitcher:
  • Fix an issue with memory allocation. This slightly improves operation speed and more helpful errors are shown.
• (E/P) Bleaching Corrector:
  • Fix error messages upon unexpected closing of the bleaching corrector.
• (E/P/L) MIP Renderer:
  • Fix improper validation of animation settings fields.
• (E/P/L) Renderers:
  • Fix freezing/error messages in custom color selector due to improper validation of input fields.
• (All) File readers:
  • Fix emission and excitation wavelengths sometimes not being read correctly from CZI files.

21.10.1p2 (16th of March 2022)

• (E/P) Deconvolution Wizard:
  • Fix an issue where the inversion of brightfield channels in a multi-channel image did not work correctly in some cases.
• (E/P/L) Object Analyzer:
  • Workflow Designer (E/P): Fix the "Experiment report" step not getting verified sometimes.
  • Fix table tooltips not working correctly when hovering over a conditions row while a column is selected.
• (E/P) Fusion Wizard:
  • Fixed an issue that prevented deconvolution templates from working in the Fusion Wizard.
• (E) Abberior Feeder:
  • Add abberior feeder toggle to the import options in the File-menu.
• (All) Non-graphical start-up:
  • Fixed a regression that blocked LASX HyVolution from working.

21.10.1p1 (8th of February 2022)

• (E/P) Deconvolution Wizard:
  • Added an editor for the numerical value of the acuity.
• (E/P) Deconvolution Express:
  • Fix regression where Airyscan images acquired with Fast-mode sometimes contained empty regions after deconvolution.
• (E/P/L) Object Analyzer:
  • Fix an issue where merging a very large number of objects could cause errors.
  • Fix computing the distance to anchor surface for the ROI, if the anchors are analyzed before the ROI.
• (L) Chromatic Aberration Corrector Wizard:
  • Fix the quick launch button of the Chromatic Aberration Corrector.
  • Fix an issue where some of the buttons for opening other tools were not working correctly in the Localizer.
  • Improved the behavior when closing the window while calculations are busy.
• (E/P) Object Stabilizer:
  • Fix an issue where model-based stabilization could produce outliers with large incorrect shifts when the GPU was enabled.
• (All) LIF file reader:
  • Fix bug when reading metadata of light sheet lif files, which caused the microscopic parameters to not be applied.
• (E/P) Microscopic parameter editor:
  • No longer show the TIRF and SMLM 3D microscope types. These types were only intended for Localizer and could cause various issues in Essential and Professional.

21.10.1p0

• (E/P/L) Chromatic Aberration Corrector
  • New estimation methods that can correct for 3-D rotation, expansion/shrinking and radial non-linear distortions in addition to a 3-D shift were added to the existing Chromatic Aberration Correction Window.
  • A new Chromatic Aberration Correction Wizard was added with more explanation, guidance on which estimation method to choose, as well as more flexibility in enabling and disabling separate components of the aberration. This tool contains a visualization of the per-channel aberration in a 3-D wireframe view.
  • Handling in templates of the new components/types of aberration that can now be corrected for.
• (E/P/L) Object Analyzer
  • Changes to the interface of the right column. In particular the channel selector now also shows the channel label.
  • Improve contrast of objects after discard or merge operations.
• (E/P) Surface Renderer
  • Changes to the interface of the right column. In particular the channel selector now also shows the channel label, and the segmentation settings are now shown for only one group at a time.
• (E/P) Deconvolution Wizard
  • The SNR is now estimated automatically. It can still be overridden if preferred.
  • Add a slider for the acuity (sharpness) of the result.
  • Minor changes to the organization of the wizard stages.
• (All) File readers
  • CZI: Improve estimation of backprojected pinhole sizes.
  • OME-TIFF: Improve reading in Micro-Manager exported files.
  • OBF: Reading of STED 3D parameter added.
• (All) File Series Tool:
  • Added option for reading array detector images from a series of images.
• (E/P) Bleaching Corrector
  • It is now possible to correct images that contain one or more channels that are unsuitable for correction (on those channels no correction will be performed).
• (E/P) Object Stabilizer
  • Add plot options to the displacement graphs so data and plots can be exported.
• (E/P/L) 3D Renderers:
  • Change zooming and rotating so that it no longer occurs relative to the center of the image, but to the center of the screen.
  • Change panning so that it no longer occurs relative to the screen, but to the image.

Minor Changes

• (E/P/L) MIP Renderer:
  • Enable greater zoom factor.
• (E/P) PSF Distiller
  • More intuitive button labelling.
  • Adjusted link to FWHM page.
• (E/P) Bleaching Corrector
  • Minor GUI adjustment for better visibility.
  • Improved input validation.
• (E/P/L) Hot & Cold Pixel Remover
  • Added a button to reset the detection sensitivity.

Bugfixes

• (E/P/L) MIP Renderer:
  • Fix rendering issue causing glitchy full rendering in timeseries.
• (E/P/L) Object Analyzer
  • Fix for the ROI shift function which had become unusable.
  • Fix an issue introduced in the 21.10.1 beta where the hue range was not applied correctly in some cases.
• (E/P) Bleaching Corrector
  • Fix for a number of table-related bugs when only correcting a range of z-planes and frames.
• (E/P/L) Multiple renderers
  • (Windows) Fix for "Domain error" pop-up that sometimes was shown when panning.
• (E/P) Object Stabilizer:
  • Fix an issue where the Object Stabilizer could crash when going back and forth between different stages.
• (E/P) Deconvolution Express:
  • Fix an issue introduced in the 21.10.1 beta where the ROI deconvolution would fail for brightfield images.
  • Fix an issue introduced in the 21.10.1 beta where the Express deconvolution would fail for Zeiss Airyscan2 Rings images.
• (E/P) Deconvolution Wizard
  • Fix an issue introduced in the 21.10.1 beta where the airyscan reduction mode could get stuck on "auto".

21.10.0p1 (7th of December 2021)

• (All) MSR/OBF reader:
  • Fix for older msr images that could cause a crash when trying to find XML metadata.
• (All) LSM reader:
  • Fix emission and excitation wavelengths not getting read in some cases.
• (E/P/L) Object Analyzer:
  • Fix a bug introduced in 21.10p0 where some filter options would not work.
• (All) Compute Engine:
  • Fix an issue where the img open, preOpen, and getFileType commands could not handle paths with a tilde (~) in it.
• (E/P) PSF Distiller:
  • Fix a link to the HIW/FWHM page.
• (E/P) Movie Maker:
  • Fix an issue where the "Surface Renderer exploration" preset would not work when preceeded by a Surface Renderer frame that uses a slicer.
• (E/P) Deconvolution Wizard:
  • STED deconvolution:
    • Fix the wizard going astray after starting the estimation in the "Estimate psf" step.
    • The "Estimate psf" step is now also available when "Expert mode" is disabled.

21.04 release

PSF Distiller

• Support for array detector images (Airyscan I & II, SPAD, etc).
  • Distill array detector PSFs from bead images.
  • Obtain even better deconvolution results on array detector images by using distilled PSFs.

• FWHM Estimator:
  • Automatically find the FWHMs of the distilled PSFs and compare them with their theoretical counterparts.
  • Inspect the lateral and axial FWHMs of each independent channel and detector.
  • Export the FWHM data to .csv or .txt files.

Deconvolution Express

• Improved interactivity and contrast handling
• Automatic selection of an interesting region of interest

Image Stitcher & Deconvolution

• New option to prefilter image intensities exclusively during the optimization stage.
  • This is useful for reducing the effect of hot/cold pixels in the final tile positions.
• New option to skip the optimization step for directly stitching the data with the input tile offsets.
• The flat field and dark frame images used for manual vignetting correction can now have any number of planes and channels.
• Support for Abberior Facility Line .obf files.

Object Analyzer Advanced

• Create analysis workflows with the new Workflow Designer. In the Workflow Designer the various tasks constituting a Workflow are shown as an interactive block diagram. Drag and drop tasks to create a Workflow.
• Load/save workflows as templates. Reproduce the experiment and image analysis with these workflow templates.
• List of operations:
  • Set and customize segmentation groups, Regions Of Interest (ROI), visualization parameters, object anchors, parameter filters, general analysis options, experiment reports, table exports.
• Use predefined Workflows for some common experiments, like measuring geometric properties of objects, colocalization analysis, or computing total volume.

Workflow Processor

• New task for configuring file series:
  • Selecting a file from a series loads the File Series tool for further customization of the channels, time frames, and slices.
  • Selecting a container file (e.g. .czi, .lif) allows for further inspection and selection of its contents (sub images).
• Renamed Task Designer as Workflow Designer.
• New option to edit existing workflows.

Minor changes

• (All) Huygens Everywhere
  • Optimize server connection.
• (All) Abberior OBF files:
  • Support for reading of v6 obf files.
  • Better handling of Facility Line meta data.
• (All) Nikon ND2 files:
  • Enhanced support for reading nd2 files on Windows and Linux.
• (All) CZI reader:
  • Rename tag 'AirySheppardLines' as 'MergedAiryFastMode' for Airyscan2 fast mode images.
• (E/P) SFP/MIP/Surface renderer
  • Add Orientation indicator to the canvas.
• (E/P) Object Analyzer Advanced
  • The "Analyze ROI volume" option now reports the segmentation conditions and object count in the table.

Bug Fixes

• (All) GPU processing:
  • Fix "Out of memory" errors on some Windows systems which could occur when another application was using GPU memory simultaneously.
• (All) Leica lif files:
  • Fixed regression where sometimes STED parameters were not fully read in.
• (E/P) Object Analyzer Advanced
  • Removed the dysfunctional option to set anchors by filtering all time frames or detectors.

21.04.0p6 (8th September 2021)

• (All) GPU processing:
  • For Windows and Linux, centralize the NVIDIA cache in the Huygens installation folder. This fixes potential delays when launching Huygens.
• (All) MSR/OBF reader:
  • Fix issue for Abberior v6 obf files where decompression to voxeldata failed for large chunks.

21.04.0p5 (30th August 2021)

• (All) Histogram computation:
  • Fixed the GPU version of 1D/2D histogram for signed and unsigned integer images with voxel values smaller than 0 or larger than 32767.
• (All) GPU Cuda code:
  • Fixed potential bugs involving out-of-bounds memory access.
• (All) OME TIFF reader:
  • Fixed reading file series, where the Huygens image allocated was too small to contain the series.
• (All) ICS reader:
  • Fixed handling of the parameters most recently introduced in the ICS library.
• (All) Linux installer:
  • Fix desktop launchers occasionally showing disabled system icons instead of the Huygens products.
• (E/P/L) Workflow processor:
  • Fixed the order of dimension conversion and deconvolution in the backend. It now correctly has the intended order of conversion before deconvolution.
• (E/P/L) ND2 reader for Windows and Linux:
  • Improved how data coordinates are handled, this was part of the problem for previous ND2 reading issues and should fix the current issue of XY slices getting repeated over Z in some images.
• (E/P/L) Object Analyzer:
  • (E/P) Prevent multiple Workflow Designers being opened at the same time.
  • (E/P) Performance improvements for computing colocalization statistics for many objects.
  • (E/P/L) Fix object count being off by one when watershed segmentation is used.
• (E/P/L) Main window:
  • Fix thumbnails becoming unresponsive in some cases.
• (E/P) Stitcher:
  • Remove superfluous question about converting tile data from channel spec packed to stacked.
• (E/P) SFP renderer:
  • Fix issue where resizing the window before the SFP renderer is fully loaded could cause the renderer to freeze.
• (E) Main window:
  • Made it easier to acces the Decon Express by adding a button to it in the main window.
• (P) Main window:
  • Fix the mouseover tooltip of the GPU status button sometimes displaying outdated information.

21.04.0p4 (19th July 2021)

• (All) CMLE deconvolution:
  • Increase the estimated amount of memory needed. This can result in more bricks being used. It prevents CPU/GPU data migration from slowing down the deconvolution.
• (All) Deconvolution on Mac OSX:
  • Let the deconvolution result be in floating-point data if the amount of memory allows it, in the same cases as on Windows. This prevents loss of precision by unnessary rounding to integer-typed results.
• (E/P/L) User interface:
  • Fix an issue with using the mouse wheel to scroll on Windows.
• (E/P/L) PSF Distiller:
  • Fix excessive memory usage and computation that could also lead to a crash, when multiple beads are accumulated on Windows without GPU.
• (E/P/L) Object Analyzer:
  • Fix the statistics pop-up sometimes not displaying analysis statistics correctly on Windows.
• (E/P/L) Track analyzer:
  • Fix not being able to complete a drawn boundary with double click.
• (E/P/L) ND2 reader for Linux and Windows:
  • Fix an issue where the Z planes and time frames got mixed up.
• (E/P/L) Workflow Processor:
  • Fix an issue when saving tiffs with long names. It will now truncate long names.
• (E/P/L) Slicer:
  • Fix memory leak when the same image was plotted twice.
  • Added the option to disable automatic generation of a new slicer to show the line profile plots in.
• (E/P/L) Default metadata:
  • The default emission wavelenghts for 3-channel images without metadata have changed to a red, green and blue wavelength. This makes actual RGB images recognizable and uses wavelengths of commonly used fluorophores.
• (E/P) Image Stitcher:
  • Fix regression introduced in the previous patch in the form of an occasional message 'missing value to go with key'. This occurs to some tiles missing both proper meta data and name patterns indicating the offsets.

21.04.0p3 (28th June 2021)

• (All) Huygens Everywhere:
  • Fix the use of svi.nl passwords containing special characters.
• (All) Cropper / Compute Engine:
  • Automatic cropping now crops the axial direction less aggressively for widefield and brightfield images.
• (All) GPU support in Windows:
  • Fix regression in version 21.04 that resulted in poor GPU performance.
• (All) MSR/OBF reader:
  • Fix memory leak.
• (All) ND2 reader:
  • Fix swapped Z/T dimensions in some images.
• (All) Compute Engine:
  • Fix the watershed command sometimes failing for images that segment into a large number of objects.
• (E/P/L) Twin Slicer:
  • Fix contrast not being applied correctly when the contrast option "Custom compression" is selected for the first time.
• (E/P/L) Object Analyzer:
  • Fix object count and anchor count not being displayed after clearing the table.
  • Fix an issue where under rare circumstances clicking an object would not trigger an analysis of the object.
• (E/P) Deconvolution Express:
  • Fix for the error message 'can't read "orgSizeS": no such variable'.
  • Fix the wizard showing an error after cancelling the deconvolution.
• (E/P) Fuser:
  • Fix the application of the scale parameters (stretching/compression) to the images.
• (E/P) Batch Feeder:
  • Fix Batch Feeder initializing very slowly on Windows when a directory containing a large number of tiff files is being watched.
• (E/P) Image Stitcher:
  • Fix for tiles missing both proper meta data and name patterns indicating the offsets.

21.04.0p2 (9th June 2021)

• (All) LSM reader.
  • Fix regression in reading meta data.
• (All) CZI reader:
  • Fix for Airyscan2 (AirySheppardRings) images which would occasionally not open.
• (E/P/L) Object Analyzer and (E/P) Surface Renderer
  • Fix an issue where the software could hang when using watershed segmentation.
  • Fix the sigma slider not updating when switching channels.
• (E/P) PSF Distiller:
  • Fix regression leading to too small PSFs for beads from Spinning Disk Confocal Microscopy.
  • Add guidance to avoid images from Array Detector fast modes.
• (E/P) Workflow Processor:
  • Series files opened with the "Select image series" task are now split over multiple workflows when possible, this improves processing speed when multiple cores are available.
  • Added task information to preview thumbnail names.
  • Fix an issue with the Quick Select menu in the "Set microscopic parameters" task.
  • Fix an issue with the "Set microscopic parameters" task UI not updating depending on it being in or out of the workflow.
• (C) Huygens Core:
  • Fix Huygens Core sometimes not starting when the -gui flag is used.

20.10 release

Huygens Everywhere & new style Huygens Floating licenses

• New user portal for license administration. Log in with your svi.nl account. Add/remove users to/from your licenses. Set the maximum allowed concurrency on a per-user basis.
• Get your licenses and subscriptions at the SVI webshop.

Huygens Professional & Essential

Image Restoration

• Airyscan 2: Sheppard 4-ring data now supported. If available, 32 detector raw data from Airyscan 2 is also supported.
• Brightfield: add 'ctm' algorithm to Workflow Processor, Deconvolution Wizard, Decon Express, and Batch Feeder for transmitted light images. The algorithm takes care of intensity inversion, PSF calculation, background estimation, bricking, etc. Available for CPUs and GPUs.

Workflow Processor

• Replaces the Batch Processor tool in Huygens Essential, Professional and Localizer.
• Shows previews of the result image during and after processing. These previews allow you to quickly access the results in different Huygens tools.
• Create complete image processing sequences with the new Workflow Processor. In this Processor the various stages constituting a Workflow Task are shown as an interactive block diagram. Drag and drop stages to create your Workflow.
• List of operations:
  • Conversion of image dimensions, cropping (both with templates and on auto mode), correction of hot/cold pixels, stabilization of Z stacks, baseline adjustment, deconvolution (including bleaching correction and background subtraction), stabilization of time series, correction of chromatic aberrations, correction of Z drift.
• Additional features:
  • The saving directory and format can be set for individual tasks
  • Conversion of file formats in batch mode.

Huygens Python scripting

• Added Python scripting capabilities to Huygens Professional, Huygens Localizer, and Huygens Core
• Allows manipulation of images and SMLM localization tables with the full set of operations that are also available in Tcl.
• Scripting can be performed directly in the Huygens interface or by using .py scripts loaded from the command line.
• Additional Python modules can be imported for even more options.
• Note: currently supported on Linux and Windows.

Image Slicer

• Renewed Image Slicer.
• Includes line plotting, movies, MIP and SUM projection modes, overlays, exports, and more.
• Improved contrast and color control.
• Improved linking of slice position, zoom, color and contrast settings with other slicers.
• Includes a 'clone' option for easy, fast replication of the slicer instance.

Minor changes

• (All) GPU support
  • CUDA versions 7.x no longer supported.
• (E/P) Object Analyzer
  • Renamed graphics pipes into segmentation groups and improved location of channel selection.
  • Watershed segmentation and garbage volume entry are now easily accessible.
• (E/P) Stitcher:
  • Clearer feedback on the progress of loading tiles.
  • One single open button for all types of files and patterns. This replaces drag&drop option introduced in 20.04.0p3.
  • Make it optional to visualize the tile guides and numbers.
• (E/P) Cropper:
  • Add support for templates.
• (E/P) Deconvolution Wizard:
  • Add visualization controls (brightness, contrast, colors, zoom, ..)
• (E/P) Batch Express:
  • Renamed as Batch Feeder.

Bug Fixes

• (All) CZI reader:
  • Fix potential shift in excitation wavelengths.
• (All) TIFF reader/writer:
  • Fix performance regression on Windows.
• (E/P) Cropping tool:
  • Fixed an issue with the preview.
  • Fixed an issue with the placement of the MIP sliders after resizing the window.
• (E/P) Fuser:
  • Made finding the axial shift along the main axis of rotation more robust.
• (E/P) Object analyzer and hybrid renderer:
  • Changed the definition of the seed level when watershed segmentation is used. The seed level now refers to the intensity level that must be reached in the original image, rather than the Gauss-filtered image. This makes the results before and after watershed segmentation more comparable and fixes issues with small objects disappearing when using watershed segmentation.
• (E/P) Stitcher:
  • Fix excessive memory allocation when working with images of unsigned integer type.

20.10.1p3 (8th April 2021)

• (All) Huygens Everywhere:
  • Indicate the progress of contacting the servers in the Login window.
• (All) GPU Processing:
  • Fix issue with loading the enabled devices from the preferences.
• (All) Updates:
  • Fix notification when the GDPR message has not yet been accepted.

20.10.1p2 (8th March 2021)

• (All) VSI reader:
  • Fix for loading the first sub image from Tcl scripts without specifying the sub image index.
• (All) CZI reader:
  • Don't map channels with unspecified microscope types.
• (All) HDF5 reader:
  • Significantly faster on Windows.
• (All) MSR/OBF reader:
  • Significantly faster on Windows.
• (All) GPU Processing:
  • Accept other names for the GTX 1650 card.
  • Implement missing sub cases of the image histogram 'hist' operation.
  • Implement the 'roiStat' operation.
• (All) Deconvolution:
  • Fix small memory leak in CMLE.
• (E/P/L) Huygens Everywhere:
  • Use port 9118 on the second server from the list. This should help in making it work with proxy servers and some firewalls.
  • Don't throw an error if there are multiple attempts to create the login window.
  • Fix client hanging on broken communication.
• (P/L/C) GUI:
  • Fix ocassional error message on Huygens shutdown caused by memory widget updates after GUI destruction.
• (E/P) Stitcher:
  • The flat field and dark frame images used for manual vignetting correction can now have any number of planes and channels.
• (E/P) Movie Maker:
  • Fix errors in some presets.
• (E/P) PSF Distiller:
  • More accurate normalization of multi channel PSFs.
• (E/P) Workflow Processor:
  • Better handling of TIFF types for saving data.
• (E/P) Object Tracker:
  • Fix rendered image and overlay when drawing ROIs.
  • Add an option to import ROIs from the main window.
  • Make the Object Tracker available in Huygens Localizer.
• (P) Operations Window:
  • Save the proper SNR value and tag to deconvolution templates.

20.10.1p1 (January 27th 2021)

• (All) Compute Engine:
  • Fix an issue where repeated use of some modules during one session could cause "Cannot handle more strings" errors.
• (All) VSI reader:
  • Fix for Huygens crashing on opening images with missing tiles or aborted time series.
  • Fix for missing planes in files with very large pyramids and Z dimension > 1.
• (All) CZI reader:
  • Fix regression for files reporting custom but empty compression schemes.
• (All) ND reader:
  • Fix for loading the first sub image from Tcl scripts without specifying the sub image index.
• (All) OBF/MSR reader:
  • Fix for cases where the meta data is split across multiple annotation nodes.
• (All) GPU support:
  • Fix for theoretical, multichannel PSFs with spherical aberration.

20.10.1p0 (January 12th 2021)

• (All) GPU support:
  • Raise the limit for GPU memory on 'Small' GPU cards from 3 to 6 GB.
• (All) OME-TIFF reader:
  • Fix potential crash on Slidebook images.
• (All) Compute Engine:
  • Improve event handling. Solve warning about 'too many events in buffer'.
• (All) VSI reader:
  • Add support for pyramid RGB files.
• (All) LIF reader:
  • Fix interpretation of meta data for non standard "," as decimal point indicator.
  • Improve reading of meta data for non-descanned detector channels.
• (All) MSR reader:
  • Fix potential crash on images with no meta data.
• (E/P/L) Object Analyzer:
  • The user interface (UI) has been updated:
    • The old reference cube has been replaced with a new orientation indicator, which is shown in the bottom-right corner of the canvas.
    • Settings for garbage volume and watershed segmentation are now shown beneath the histogram.
    • Settings for visualization (transparency, brightness, hue) have been moved to a separate "Visualization" tab.
    • Various other buttons in the main window have been moved to a new location.
    • The old "Conditions" row in the statistics table has been split into two rows, "Conditions" and "Findings".
  • Advanced only (E/P):
    • The functionality for creating your own experiment presets (user presets) has been expanded. The preset selection window now shows three available user presets by default, and user presets can be edited from within this window.
    • When creating a 360° movie, the renderer will now use the segmentation conditions you specified.
• (E/P) Decon Express:
  • Fix potential abrupt termination on Array Detector images.

20.10.0p3 (15th December 2020)

• (All) GPU support:
  • Add support for the 'GeForce GTX 1660 Super' card without a GPU license.
  • Disable the GPU system when any module (ptx file) fails to load, preventing error messages about NULL modules later on.
  • Check for the cards with Compute Capability between 3.0 and 3.5 that are no longer supported by Huygens 20.10. Give a proper error message instead of letting GPU operations fail later on.
• (All) Array Detector Deconvolution:
  • Improve results when on GPU mode.
• (All) OME-TIFF reader:
  • Fix error for tiled files containing misleading meta data about dependencies with other files.
• (E/P/C) Batch Processing:
  • Fix propagation of quality thresholds for GMLE.
• (E/P) Chromatic Aberration Corrector:
  • Improve matching template channels to image channels for microscope types 'Array Detector' and 'Rescan'.
  • Fix potential issue when loading two or more different templates in one tool instance.
• (E/P) Object Analyzer:
  • Fix reported colocalization volume and sum when on GPU mode.
• (E/P) Image Stitcher:
  • Fix rerouting of some CZI files containing tiles which did not prompt questions about loading in the Stitcher.
• (E/P) Slicers:
  • Fix occasional issue with limiting zoom factors.

20.10.0p2 (25th November 2020)

• (All) GPU support:
  • Remove inaccurate message "Processing on CPU" from CMLE while Huygens was using the GPU.
  • Update the tooltip text on the GPU status icon in Huygens Professional when the GPU has been successfully initialized.
  • Warn about a graphics driver that is too old for the Cuda Toolkit version when the Cuda Toolkit version is 9 or lower.
• (All) CZI Reader:
  • Fix potential memory overflows that could lead to a crash.
• (E/P) Image Segmentation:
  • Fix interpretation of the seed value in watershed segmentation.
• (E/P) Chromatic Aberration Corrector:
  • Fix glitch in template selection panel.
• (E/P) Deconvolution Wizard & Brightfield Deconvolution:
  • Fix for when brightfield channels are skipped.
• (E/P) Image Renderers (MIP, SFP, Surface):
  • Faster for large images. Added an option to the Huygens Preferences to dynamically adapt the image size.
• (E/P) Image Thumbnails:
  • Fix slider style.
  • Now render faster for large images.
• (E/P) SFP Renderer:
  • Fix incorrect negative values for tilt and twist.
• (E/P) Workflow Processor:
  • Add an option to select all images in a folder.
  • Switch to other presets and back without losing the edited parameters.
  • A clearer channel selection in the Deconvolution Template editor.
  • Fix potential empty thumbnails on Windows.
• (P) Main Menu:
  • Fix 'Workflow Processor' entry which only got enabled on selecting an image.

20.04 release

New subscription based model to work with Huygens Essential and Localizer Everywhere

• Use Huygens on any computer by logging in to Huygens Everywhere.
• Just install, log in with your www.svi.nl credentials.
• Monthly payment via PayPal

Huygens Professional & Essential

• Image Restoration:
  • Improved GPU utilization for large images, leading to larger bricks and improved performance (up to 5x in some cases).
  • Improved handling of severely undersampled images.
  • Improved handling of spinning disk images with large refractive index mismatches.

• Surface Renderer and Object Analyzer:
  • Greatly improved performance of watershed segmentation by adding GPU utilization and improving multi-core CPU utilization.
  • Tweaked the interpretation of seed and garbage volume when using watershed to be more consistent. Seed and garbage volume checks are now applied to split objects individually.

• Huygens Stitching & Deconvolution Wizard:
  • Full stitching support for Abberior STEDYCON .obf files.
  • Use any selection of multiple files from disk directly in the stitcher with default layouts.
  • Support for LaVision OME-TIFF tile-series with [00 x 00] filname patterns.
  • Add possibility to disable alignment in the Z direction.
  • Significantly faster for scenes with 100+ tiles.

• Colocalization Analyzer:
  • Expand GPU support to all datatypes (byte, signed integer, unsigned integer).

• New Thumbnail options:
  • Switch from 3D perspectives to slicer views. Slice through 3D thumbnails in X, Y, Z.
  • Also Huygens Professional shows now a button bar for each thumbnail with options for color mode, edit parameters, Decon Express, crop, split, and delete.

Huygens Localizer

• Add color-coded time rendering mode that renders spots in a color according to the frame number they were found in. This visualizes object or stage drift and can help identify other imaging issues.

Minor changes

• (All) Abberior STEDYCON:
  • Reading of separate Tiles.
  • Better handling of XYZ vs XYT images.
• (All) HDF5 reader/writer:
  • Upgrade to a new release of the hdf5 library.
• (E/P) Huygens main window:
  • Histogram tab is now shown first by default and supports multichannel images.
• (E/P) File series tool:
  • Allow for two independent indexes coding X and Y tile coordinates for stitching.
• (P) Non existing destination images are now created automatically by all commands.
  • Because of this the 'a, b, c, psf' buffers are no longer shown on startup.
• (L) Huygens Localizer:
  • Greatly improved performance of the localization table reader.

Bug Fixes

• (All) LIF, OME, MSR readers:
  • Fix small memory leaks.

20.04.0p5 (15th October 2020)

• (All) File writers:
  • Fix partially empty tiff files when saving large multi-channel images to a tiff-based format.
• (All) File readers:
  • Fix potential hard errors in MSR reader. Improve reaction times in Windows.

20.04.0p4 (14th September 2020)

• (All) GPU Support:
  • Show a pop-up when the GPU initialization is performed for the first time (after an update of Huygens or the graphics driver) if it can take a long time.
  • The RTX 3070, RTX 3080, and RTX 3090 can be used with the g1, g2, and g2 flags respectively.
  • Fix diadic operation for complex multiplication.
• (All) File readers:
  • Fixed ome-tiff reader issue when reading multiple planes of a series.
  • Fixed hdf5 reader for complex-valued images.
• (E/P/L) Object Analyzer:
  • Fix CPU/GPU regression that made it impossible to discard objects.
  • Fix option "ROI>set>Envelop anchors/make coincide with anchors".
• (E/P/L) Huygens Everywhere:
  • Added support for remotely logging out a session owned by the same user. This makes it easier to manage accounts with a maximum concurrency larger than 1.
• (E/P/C) GMLE Deconvolution:
  • On request, stop the entire process rather than only the current brick.

20.04.0p3 (29th July 2020)

• (All) GPU support
  • When logging in to Huygens Everywhere allow for at least small GPUs even when not included in the account.
  • Prevent an error on Huygens shutdown about a failure with a destroyed Cuda context.
  • Add more elaborate CUFFT versus Cuda Driver version checks, results being displayed in the GPU Status Window.
• (All) OSX file dialogs:
  • Change default preference to use the native file dialog.
• (All) Huygens Everywhere:
  • Fix for accounts with long e-mail addresses.
• (E/P) Drag & drop / Stitcher:
  • When using drag & drop on multiple files a new option is included to load them directly into the stitching tool or not.
• (E/P) PSF Distiller
  • Fix coloured legend showing qualifiers for beads in multichannel images.
• (E/P) Communication with Leica LAS X.
  • Fix image imports.

20.04.0p2 (26th June 2020)

• (All) Huygens Everywhere
  • Avoid long timeouts when IPv6 networking appears to be present, but is not actually working.
  • Enable 'Remember me' also when the service is overridden by another type of license.
• (All) GPU support.
  • Raise an error if the Cuda Toolkit is too new for the graphics driver.
  • Fix support for CUDA 11.
• (All) Compute engine:
  • Fix potential issue in some operations where the same image is used for input/output.
• (E/P/L) Thumbnails:
  • Fix for very long names.
• (E/P/L) File dialogs:
  • Default to the native Windows file dialog, also when using Huygens on night mode.
  • Improve visibility of selected items when on night mode.
• (E/P) Render panel.
  • Fix glitch when on freeware mode.
• (E/P) Batch processor.
  • Fix support for GMLE deconvolution algorithm.

19.10 release

Huygens Localizer

• New option for analyzing astigmatic 3D SMLM data:
  • Support for CPU and GPU.
  • PSF Distiller for obtaining nearly noise-free 3D SMLM calibration data from fluorescent beads.
  • MIP Renderer with depth-coded color modes.
  • 3D object analysis.
• New Batch Processor for 2D SMLM data:
  • Process large amounts of data in batch mode.
  • Support for CPU, GPU, and multi GPU.
  • Optionally save the localization tables and renders of each batch job.

Huygens Professional & Essential

• New Huygens Fuser:
  • Replaces the Fusion Wizard which can now be found in Tools -> Legacy.
  • Manually align multi-view light sheet images with direct visual feedback.
  • Fully tunable automatic optimization on manual alignment.
  • Pre-cropping result image for a more memory efficient and faster fusion.

• Many new features in 3D rendering and performance improvements:
  • New CPU implementations with perspective for all renderers to allow seamless switching between CPU and GPU.
  • Freely adjustable lighting direction in the SFP Renderer, as well as a camera-tracking mode.
  • The ability to add an iso-surface to a scene in the SFP Renderer, allowing you to highlight important features.
  • The ability to add up to 6 cutting planes to a scene in the SFP Renderer, each with a configurable orientation and offset. Cleanly cuts away SFP material and iso-surfaces.
  • The slicer in the Surface Renderer now actually cuts away surfaces.
  • New depth-coded color mode in the MIP Renderer. Each point is assigned a hue based on either the Z-position or the distance to camera.

• New render panel in main window:
  • Real time views for the selected image thumbnail showing 3D scenes from the MIP, SFP and Surface renderers, plus the 2D plane from the center of the stack.
  • The views also serve as links to the corresponding tools (MIP renderer, SFP renderer, Surface renderer, Twin Slicer).
  • Optionally collapse/expand the render panel.

Minor changes

• (All) Abberior STEDYCON:
  • Better decisions in case of occasional communication problems (e.g., network issues).
  • Improved deconvolution of images with extremely high saturation factors.
  • The saturation factors reported via the Parameter Editor, Huygens Tcl commands, etc., now reflect the values used by the deconvolution and the Abberior acquisition software.
• (All) License Manager:
  • New possibility to add/remove licenses without the need to restart Huygens.
• (All) GPU support:
  • Even more functionality is now supported by the GPU (qgauss filter, resample, binning).
  • Automatic migration of images to and from the GPU makes better decisions.
  • New GPU status indicator in the case of a missing CUDA Toolkit.
• (All) Parameter Editor and related Huygens Tcl commands:
  • Added new microscope types TIRF and SMLM 3D for Localization microscopy (no deconvolution).
• (All) TIFF reader:
  • Much faster loading of TIFF series on Windows.
• (E/P) Decon Express & Batch Express:
  • Better decisions for images with all parameters verified by the user (see Parameter Editor).
• (E/P) PSF Distiller:
  • New colored overlay showing accepted versus rejected beads.
  • Report on the reasons for rejecting each discarded bead.
  • Larger thumbnails for candidate and accumulated images.
• (E/P) Object Tracker/Track Analyzer:
  • Show total track length of joined segments.
• (E/P) Slicers:
  • Rename gamma options 'Stretching' -> 'Apply to', 'Global' -> 'Full image', 'Per screen' -> 'Displayed region'.

Bug Fixes

• (All) Deconvolution:
  • Increase accuracy of non-widefield theoretical PSFs even further for extreme cases.
• (All) File readers on Windows:
  • Fix the calls to the OS in order to avoid the 'Not responding' stamp.
• (All) 'avgspheres' command:
  • Fix small memory leak.
• (All) DV/MRC Reader:
  • Distinguish better between reading tiled images and time series.
  • Improved reading of tile offsets.
• (E/P) Analyzer tools:
  • Update ROI selection to work with perspective rendering. An ROI is now represented by a shallow cone.
• (E/P) Cropper:
  • Fixed unexpected frame-number rounding behavior when trimming very small time series.
• (E/P) Stitcher:
  • Fixed occasionally incorrect patterns after loading tiff series.

19.10.0p3 (26th March 2020)

• (All) LIF reader:
  • Fix for meta data of TIRF data sets.
• (All) HDF5 reader:
  • Fix potential errors on unknown meta data fields.
• (All) Colocalization analysis:
  • When RBNCC is selected do the processing on the CPU.
• (P/C) 'genPsfExpl' command:
  • Made 'stedInhibContr' parameter optional.
• (E/P) Stitcher:
  • Fix regression for FOVs showing tiles with lots of signal as well as tiles with only background and noise.
• (E/P) 2D visualization tools:
  • More defensive against potential errors on image statistics.
• (E/P) SFP renderer:
  • Add missing parameters to movie transitions of small images.
• (P) Operations Window:
  • Rename 'regularization' as 'signal/noise ratio' where needed.

19.10.0p2 (27th January 2020)

• (All) Deconvolution:
  • Fix regression in high quality ICTM algorithm.
  • Fix reading of default template values for cropping and stabilization tasks.
  • Better handling of Array Detector time series.
  • Better handling of 1-plane widefield images.
• (All) 'stat' command:
  • Add GPU support for extra dimensions.
  • Fix potential out-of-bounds issue in GPU implementation.
• (All) 'gauss' command:
  • Better optimizations for 1-pixel-high images.
• (All) GPU license:
  • Grant free GPU usage to Quadro T1000.
• (All) CZI reader:
  • Only set the array detector properties when there's more than one detector.
• (All) IMS writer:
  • Fix to not write uninitialized memory to the file header.
• (E/P/C) Batch Processing:
  • More robust against 'stdout' errors potentially leading to task timeouts.
• (E/P) Main window UI:
  • Set the 'histogram' tab as the new default tab.
  • In Professional switch to the 'Task reports' tab and back to the previously selected tab automatically when there's work being done.
• (E/P) Chromatic Aberration Corrector:
  • Allow for 3 decimal point factors.
• (E/P) Deconvolution Express:
  • Fix a bug in the PPU estimator that could result in a Tcl error and no deconvolution result.
• (E/P) Batch Express:
  • Fix for irrelevant warning.
• (C) SNR estimator for HRM:
  • More accurate results.

19.10.0p1 (2nd December 2019)

• (E/P) Interactive Fuser:
  • Fix issue in background handling for the first processed view.
  • Weighted sum of local pixel value now correctly weighs the overlapping regions instead of simply adding them.
• (E/P/L) Thumbnails:
  • Improve scaling of thumbnails and reinstate 2D option for smaller thumbnails.
  • Fix 3D SMLM results sometimes only being shown as 2D thumbnails in Localizer main window.
• (E/P) Object Analyzer:
  • Include new option for filtering objects touching only X or Y borders.
• (All) RPM Installer:
  • Fix missing application menu and desktop icons after upgrading Huygens for future versions.
• (All) GPU initialization:
  • Add version check for CUFFT library and distinguish NVIDIA graphics driver Cuda version from Cuda Toolkit version in the GPU status window.
• (All) File readers:
  • Added support for stitching of LaVision OME-TIFF tile-series with [00 x 00] filname pattern.
  • Improve bit-depth checks for better reading of .czi files.
  • Fix for .dv files with 16-bit data that could not be loaded.

19.04 release

New product: Huygens Localizer! Huygens Localizer allows for easy and fast analysis of single molecule localization microscopy (SMLM) data:

• Intuitive interface.
• Automatic plots showing:
  • Bleaching patterns in the time series.
  • Particle counts per time frame.
  • Histograms of particle positions, intensity, offset, and uncertainty.

• CPU and GPU support for fast analysis of SMLM data:
  • Background estimation
  • Spot detection
  • Localization
  • Rendering

• Automatic drift correction and PPU estimation.
• Export a table of localizations or use the interactive renderer to create super-resolution images.

• Analyze SMLM super-resolution images.
  • Properties of the particles: position, volume, center of mass, surface, length, principal axes, etc.
  • Study groups of particles: distance to reference objects, intersection of objects in different channels, correlation, etc.

Huygens Professional & Essential

• Abberior (STEDYCON) image feeder option:
  • Efficient data exchange from STEDYCON to Huygens.
  • Improved meta data interpreter.
  • Improved handling of single plane STED data.

• GPU acceleration of
  • MIP, SFP (see below), and Surface renderers.
  • Many basic image operations (arithmetics, masks, thresholds, etc).

• Complete overhaul of the SFP renderer:
  • Fast rendering on GPUs.
  • Much reduced memory usage.
  • New CPU functions.
  • GUI supports new lighting and shading options.

• New Interactive 3D Fusion option (release candidate):
  • The tool is now in beta-testing phase, thus not yet in production.
  • Manual approximate registration with the possibility for automatic fine tuning.
  • Deconvolve light sheet views while fusing them.

Minor changes

• (E/P) Batch Express:
  • Add all output formats supported by Huygens.
• (E/P) Preferences:
  • Ability to show only the beginning, end or both ends of long image thumbnail names.
• (E/P) Colocalization Analyzer:
  • Addition of High Quality rendering option in the visualization tabs in Advanced and Compact modes.
• (E/P) File open dialog:
  • Double click to instantly select and open a sub-image.
• (E/P) Stitcher:
  • Add support for array detector images.

Bug fixes

• (All) OBF and MSR readers:
  • Fix support for unsigned integer datatype.
• (All) Image names:
  • Better handling of long image names in 'image create'.
• (All) 'getframe' command:
  • Prevent command from working in-place.
• (All) GPU processing:
  • Initialize the GPU memory when allocating new images.
• (All) LIF reader:
  • Fix case where the file XML contains the history and parameters of the parent images.

19.04.0p6 (24th July 2019)

• (All) GPU Processing:
  • Disable unintended GPU use by large median filters.
• (E/P/C) Colocalization Analysis:
  • Fix minor memory leak.
  • Fix collision with the report of images open in Huygens.
• (E/P/C) CMLE:
  • Fix regression on the padding of Widefield images with no spherical aberration.
• (E/P) Object Analysis:
  • Fix highlighting, selecting and marking objects when rendering on high quality mode.

19.04.0p5 (17th July 2019)

• (All) File readers:
  • Fix for uncommon ICS files missing the 'sensorChannels' parameter.
  • Fix for file types containing sub images with curly braces.
  • Fix for reading CZI Airyscan 2 files.
• (All) CopyStretch ('cs') command:
  • Fix for the 'float -> byte' and 'complex -> byte' configurations.
• (All) GPU Processing:
  • Add the NVIDIA "SUPER" cards.
• (E/P/L) Filter commands:
  • Update cached image range used for image visualization.
• (E/P/L) File Drag&Drop:
  • Fix for image names with special characters and patterns.
• (E/P/L) Object Analyzer:
  • Clear removed objects which remained visible during analysis.
• (E/P) Deconvolution Wizard:
  • Fix unimportant error message shown while loading templates.
  • Fix image stabilization of mixed STED/confocal or multichannel STED images.
• (E/P) Deconvolution Express:
  • Fix potential error occurring when all GPU memory is used.
  • Show message when specific channels can't be processed due to lack of license.
  • Fix link to Twin Slicer. Opening the raw and deconvolved images in the Twin Slicer via the Deconvolution Express link should now show both images.
• (L) Export tables:
  • Add option to toggle meta data export.
• (L) Localization Analyzer:
  • Fix error when no options are selected in the candidate stage.
• (L) Mac OS:
  • Add Localizer logo replacing the SVI logo.

19.04.0p4 (27th June 2019)

• (All) GPU processing:
  • Relax the limit for the amount of extra memory that the cuFFT library is allowed to use to in order to use a regular 3D FFT in Cuda Toolkit version 10.1 update 1.
• (All) Deconvolution:
  • Increase accuracy of non-widefield theoretical PSFs even further for very extreme cases.
• (All) User preferences:
  • Fix default directory for saving images from within the Track Analyzer.
  • Fix inconsistent behaviour in the GPU window.
• (All) 'ctm' command:
  • Fix the ctm command to not return an error caused by parsing sn and snr options that do not exist for this command.
• (L) Localizer:
  • Keep the render button always active.
  • Fix occasional error in drift correction.
  • Fix center and fit after crop.
  • Fix histogram of multi channel images.
  • Starting the tool via a right-click incorrectly skipped the microscopic parameter check.

19.04.0p3 (3rd June 2019)

• (L) Installer:
  • Added code signing for Localizer.
• (All) File readers:
  • Fix file read failures in the dv/mrc reader (due to the use of uninitialized memory).
  • Fix the hdf5 file reader when reading single-channel hdf5 files written by other software.
• (E/P) Batch Processor:
  • Fix different handling of microscopic parameters depending on how the template is loaded.

19.04.0p2 (21st May 2019)

• (All) Windows OS:
  • Remove occasional KMP warning about load balancing of threads.
• (All) User Preferences:
  • Add option to enable/disable dynamic thread balancing.
• (All) GPU processing:
  • More lenient GPU license limits w.r.t. amount of VRAM (see GPUCards).
• (All) Gaussian filtering:
  • Increase performance of 'qgauss' for several CPUs and image geometries.
• (All) ND2 reader (Linux/Mac):
  • Fix for uncommon dimensions.
• (E/P/L) GPU processing:
  • Prevent "invalid data spec" error in operations where the 'cp' command is used on the GPU.
  • Show several secondary messages as warnings instead of as errors.
• (E/P/L) Cropper:
  • Fix some unusual inconsistencies in the cropping box and spinboxes.
• (E/P) MIP renderer:
  • Fix occasional off-centered scene.
• (E/P) Colocalization Analyzer (all forms):
  • Fix widget not showing completely due to lack of space.
• (C) SFP top views:
  • Remove the SVI logo from the scene table.
• (L) Localization Analyzer:
  • Fix optional histogram in the segmentation pane.
• (L) Localizer:
  • Add option for higher accuracy fits (see Particle localization -> Expert -> Fitting).
  • Progress bar shows progress more often.

18.10 Release

Huygens Professional & Essential

• Array Detector deconvolution option:
  • Airyscan (including Fast Mode)
  • NanoSPAD array
  • Generic Array Detector
  • Support for CPU and GPU.
  • Processing tools: Deconvolution Wizard, Deconvolution Express, Operations Window, Batch Processor.

• Array Detector Visualization options:
  • Slicers: Slicer, Twin Slicer, Orthogonal Slicer.
  • Renderers: MIP, SFP, Surface Renderer.

• Array Detector Analysis options:
  • 1D Histogram, Nyquist, Statistics, Object Analyzer.

• Rescan Confocal Microscopy (RCM) deconvolution option

• New in the Colocalization Analyzer:
  • Wizard mode
  • Advanced mode
  • GPU support for float images

• Light Sheet Fusion Wizard
  • New Z calibration checker tool
  • Improvements in speed and memory usage

• Added in File Reader:
  • Abberior .MSR
  • Support for Array detector file formats: CZI, ICS, HDF5
  • Leica LIF files: read files that contain both tiles and light sheet views.

• Improved Speed in Surface Renderer, Object Analyzer.

Minor changes

• (E/P) File readers/writers:
  • More responsive GUI on Windows.
• (E/P) Stitcher:
  • Add option to convert the data type of the resulting image.
• (E/P) 2D thumbnails:
  • Render the X and Y physical sizes instead of the number of pixels.
• (E/P) Slicer:
  • Update GUI.
• (E/P) Object Tracker:
  • Correctly show the Region Of Interest (ROI) visualization when importing into the object tracker.
• (E/P) Object Analyzer:
  • Add button to reset segmentation threshold slider to initial value (Otsu's method).

Bug fixes

• (All) File readers on Windows:
  • Fix long wait times when there's only 1 thread available.
• (All) OME XML file reader:
  • Improved meta data interpreter.
• (E/P) Colocalization Analyzer:
  • Fix for single object analysis not always reporting all statistics.
• (E/P) Object Analyzer:
  • Fix for slightly different initial values of segmentation threshold between primary and secondary pipe.

18.10.0p8 (25th April 2019)

• (All) MSR file reader:
  • Fix support for unsigned integers.
• (All) LIF file reader:
  • Fixes for sub images which contain the XML of the previous parents.
• (All) Main product window:
  • Show the version number and product name on the top bar.
• (All) 'multiMIP' command:
  • Fix memory buffer initialization error in "sum" mode.
• (All) 'resample' command:
  • Fix Z bounds.
• (All) GPU preferences:
  • Fix saving a disabled GPU device.
• (All) CopyPart 'cp' command:
  • Better balance to decide between CPU and GPU.
• (All) 'phaseCorr' command:
  • Fix output of the GPU implementation for some unusual geometries.
• (All) Filter commands:
  • Protect against GPU execution of non implemented filters.
• (All) 'stat' command:
  • Fix small memory leak.
• (E/P) Image Stitcher:
  • Fix support for array detector images.
• (E/P) Fusion Wizard and Deconvolution Wizard:
  • Fix error on plotting intensity profiles.
• (E/P) Surface Renderer and Object Analyzer:
  • Faster start up.
  • Fixes in the GPU labeler for specific image geometries.
• (E/P) Decon and Batch Express:
  • Fix potential error in interpretation of extremely high SNR values.
• (E/P) Slicer and Operations Window:
  • Fix brightness button.
• (E/P) Colocalization tools:
  • Increase accuracy of render controls.

18.10.0p7 (27th February 2019)

• (All) GPU support:
  • Cleanly free the GPU memory still in use by images when Huygens is closed.
  • Initialize GPU memory on image allocations.
  • Fixes for mirror operations running out of memory (fall back to the CPU).

• (All) Image Stabilization:
  • Lower memory consumption.
  • Change the name of the tight cropping method to 'very tight'. Introduce a new 'tight' mode.

• (All) Image thumbnails:
  • Fix menu entries "save as .txt" and "save as .csv".

• (All) OME-TIFF reader:
  • Faster processing of time series.

• (E/P) Deconvolution Express & Batch Express:
  • Fixes for extremely low signal images.

• (E/P) Image Fusion:
  • Fixes in template handling.
  • Fixes in non-isosampling cases.

• (E/P) Image Stitcher:
  • When the meta data contains no tile offsets ask the user if a default layout should be used instead. The layout can then be adjusted later on in the corresponding wizard stage.

• (E/P) Batch Processor:
  • Fix regression in the chromatic aberration correction concerning rotation and scaling differences across channels.

• (E/P) Image Z2T conversion:
  • Update the image dimensions in the statistics frame.

18.10.0p6 (16th January 2019)

• (E/P) Decon Express:
  • Add a warning to notify when there's not enough memory for an image backup.
• (All) Linux (Ubuntu) installer:
  • Fixes for the Ubuntu software center tool.

18.10.0p5 (7th January 2019)

• (All) ICS writer:
  • Small adaptation in new image parameter to facilitate reading ICS files in other software.
• (All) Command interpreter:
  • Fix potential memory leak.
• (E/P) Stitcher Wizard:
  • Fix regression introduced by the new array detector templates.
  • Add workaround for stitching images from the Zeiss Z1 when the acquisition is done in 'light sheet views + tiles' mode.
• (E/P) Colocalization Wizard:
  • Fix bug where different instances of the tool could affect each other's wizard state.
• (P/C) OS X user interface:
  • Fix mangled arrow character introducing a command result.
• (C) HRM image previews:
  • Fix aspect ratio for unequal X/Y sampling.
• (C) HRM SNR estimator:
  • Fix regression introduced in version 18.10 about a "missing function argument".

18.10.0p4 (7th December 2018)

• (All) GMLE + Array detector:
  • Add support for the 'varPsf' option to deal with extreme spherical aberration.
• (All) LOF file reader:
  • Fix hard error.
• (All) Monadic operations:
  • Fixes for binary images.
• (E/P) Array detector:
  • Change text in the statistics tab "Parameter dimension size" -> "Number of detectors".
• (E/P) Twin Slicer:
  • Fixes for using the preferences in the 3rd viewport.
• (E) Thumbnail and main menus:
  • More consistent naming of menu items.

18.10.0p3 (28th November 2018)

• (All) GPU support:
  • Add support for the Nvidia Quadro RTX 4000.
  • Fix potential bug in GPU-to-GPU image copy operations.
• (All) CZI reader:
  • Improve reading of Airyscan images.
  • Add support for reading different Airyscan acquisition modes as separate sub images.
  • Add support for multi file images.
• (All) Software initialization:
  • Fix regression which prevented the CE version from being displayed at startup.
• (All) Error handling:
  • Improve error messages for invalid SNR values and image names.

18.10.0p2 (20th November 2018)

• (All) CZI reader:
  • Fix for loading Zeiss Airyscan data sets on Windows.
• (E/P) Movie Maker:
  • Fix regression in the embedded tutorial.
• (E/P) Batch Express:
  • Add support for Array Detector and Rescan Confocal Microscopy images.
• (E/P) Gallery tool:
  • Fix layout for multi detector images.
• (E/P) Batch Processor:
  • Fix button for launching the microscopic parameter template dialog.
• (E/P) Thumbnail panel:
  • Fix thumbnails with very long image names.
• (E/P) Paned windows:
  • Reinstate sash handle for easier resizing.
• (P) Histogram tab:
  • Allow for wider histograms. The control buttons can now be found under the histogram plot.

18.04 Release

Huygens Professional & Essential

• New Batch Express:
  • Automatic, instant deconvolution for all acquired images.
  • Watches selected folders for new images.
  • Loads and deconvolves images automatically.
  • Deconvolution Express in batch mode.
  • Convenient control over the processing queue.
  • Easy visualization of processed images.
  • Easy link with other Huygens tools.

• Twin Slicer:
  • New Triplet mode (in Basic Mode!).

• Hot Pixel Remover:
  • New “Cold Pixel” mode.

• SPIM/Light Sheet Deconvolution:
  • New Lattice Light Sheet modality.

• Object Stabilizer:
  • New deskew mode for Lattice Light Sheet data.
  • Ability to choose a reference frame or slice.
  • Optional iterative filtering for confocal Z-stacks.

• Colocalization Analyzer:
  • New colocalization coefficients Li's ICQ and Van Steensel's CCF.
  • More intuitive UI.

• GPU Processing:
  • New GPU image filters.
  • New GPU image copy, statistics and histogram operations.
  • New GPU slicing, multiMIP.
  • Faster deconvolution, visualization, and Deconvolution Express.

• Image Readers:
  • New native Nikon ND2 and Olympus OIR readers for Windows.

• GUI:
  • New 'right-click' pop-up menu for the thumbnails.
  • New tabs.

Huygens Professional

• Multi-GPU Processing:
  • New parallelization of the channels and/or time frames of an image over more GPUs (see Operations window).

Huygens Essential

• GUI:
  • New multiple image selection.
• Data types:
  • New option 'convert to float' in 'Tools' menu.

Minor changes

• (All) GUI:
  • The night theme is now the new default Huygens theme.
  • Improved night theme version of the open image dialog.
• (E/P) Stitcher:
  • New support for tiled DeltaVision files.
• (E/P) Object Analyzer:
  • Improved memory efficiency.
• (E/P) Bleaching Corrector:
  • More intuitive UI.
  • Enable manual correction of 3D confocal images.
• (E/P) GPU Status tool:
  • Improved support for editing the GPU device configuration.
• (E/P) Join Images tool:
  • New support for joining images along x, y, z, and t.
• (P) GUI:
  • New RAM memory widget.

Bug fixes

• (E/P) Colocalization Analyzer:
  • Improved accuracy of the Object Pearson coefficient.
  • Fix bug in the calculation of the Object Spearman coefficient using an ROI image.

18.04.1p0 (8th October 2018)

• (All) Nikon ND2 reader:
  • Fix for DLL capitalization.
• (All) LSM reader:
  • Fix for undocumented channel tags (monitor diodes > 1).
• (All) CZI reader:
  • Fix for unusual meta data strings in Spinning Disk images.
  • Fix for 'System Raw' "compression" reporting no decoding information.
• (E/P) Colocalization Analyzer:
  • Fix initialization of the threshold estimation method for unreviewed time frames.
• (E/P) Fusion Wizard:
  • Fix potential deconvolution issue on integer images.
  • Fix error on adding image files.
• (E/P) Hot & Cold Pixel Remover:
  • Fix quick launch button.
• (E/P) Wizard Stabilizer:
  • Allow tight cropping for all stabilization modes when there's no rotation.!!

18.04.0p9 (18th September 2018)

• (All) Basic operations:
  • Fix an error when copying extremely small data sets with multiple threads.
• (All) CUDA support:
  • Add GP100 GPU cards.
  • Fix potential error in mirror operation.
• (E/P) Fusion Wizard:
  • Fix several workflow glitches.

18.04.0p8 (5th September 2018)

• (All) 'estbg' command:
  • Fix silent error in the CPU background estimation of unsigned integer images.
• (All) CUDA support:
  • Add support for new NVIDIA GPU models.
• (E/P) Decon Express:
  • Faster ROI deconvolution reruns when the ROI remains at the same position.
• (E/P) Fusion Wizard:
  • Lower the memory requirements.
  • Fixes for better fusing difficult images.

18.04.0p7 (21st August 2018)

• (E/P) Communication with LAS X:
  • Fix regression in version 18.04 for successfully processing images with the Low, Normal, or High Signal strategy.
• (E/P) Preferences Window:
  • Fix regression in the window size.

18.04.0p6 (16th August 2018)

• (All) Nikon Nd2 file reader:
  • On Linux and Mac fix overflow in the product of the dimensions.
  • On Windows add Spinning Disk types.
• (E/P) Geometry conversion tool:
  • Fix modes XY(ZCh) -> XYZCh, XY(ChZ) -> XYZCh, and XY(TZ) -> XYZT.
• (E/P) 'Save As' dialog:
  • Fix action on multiple selection.
• (E/P) Microscopic Parameters:
  • Fix reading the confidence level of the T sampling from templates.
• (E/P) Decon Express:
  • Fix for multichannel STED 3X images.
• (E/P) Batch Processor:
  • Fix case where the measured PSF contains fewer channels than specified in the templates.
• (E/P) Deconvolution wizard:
  • Fix warning about background free images.
• (E/P) Stitcher wizard:
  • Fix for time series supplied in TIFF form.
  • Fix manual flat field correction for combinations of tiles and flat field images where there's a dimension mismatch of the form 'size = 0 vs size = 1'.
  • Fix quick launch button.

18.04.0p5 (12th July 2018)

• (All) CUDA:
  • Add support for potential CUDA 9.3 release.
• (All) HDF5 reader/writer:
  • More responsive GUI on Windows while reading/writing.
  • Fix reading/writing binary images.
• (All) LIF reader:
  • Fix meta data interpretation in some unusual confocal cases.
• (All) XLIF reader:
  • Fix tile reading.
• (All) ND2 reader:
  • More gracious error handling of 'preOpen' on non-Windows systems. This fixes processing ND2 files in Batch Express on Linux, for example.
  • More accurate pinhole radius calculation on Windows.
• (All) OIR reader:
  • Fix sampling sizes.
• (All) PSF distiller:
  • Fix regression where the image stabilizer could not be called from within the PSF distiller for STED beads images.
• (All) Multi MIP:
  • Fix projection along T in GPU implementation.
• (All) 2D histogram:
  • Fix missing buffer initialization in the GPU implementation which could potentially lead to an inconsistent histogram.
• (All) Resample command:
  • Fix missing initialization that could potentially lead to inconsistent results.
• (All) GPU license requirements:
  • Put the GeForce GTX 1050 with 3 GB of VRAM in the list of cards that require a small license.
• (E/P) Deconvolution wizard:
  • Fix contrast of right viewport, which could show differences w.r.t the left one.
• (E/P) Stitcher wizard:
  • Fix issue where deconvolution templates did not get loaded for Ch > 0.
• (E/P): Image Stabilizer:
  • Fix potential memory leak.
• (E/P): Cropper:
  • Prevent the use of an unsupported combination of using strides and operating on a binary source image in creating the MIP for visualization.
• (E/P) Preferences window:
  • Scale with DPI value.
• (E/P): SPIM labels:
  • Renamed as 'Light sheet'.
• (E): Thumbnail panel:
  • Fixed the update of the histogram when a new image is selected.

18.04.0p4 (25th May 2018)

• (All) QMLE/GMLE:
  • Fix potential memory leak in the GPU versions.
• (All) OIR Reader (Windows):
  • Improve interpretation of meta data values.
• (E/P) Decon Express and HyVolution:
  • Fix for a 'setBias' error message.
• (E) Thumbnail pop-up:
  • Fix broken 'Save as' dialog.

18.04.0p3 (15th May 2018)

• (All) ND2 Reader:
  • Fix for less usual combinations of dimensions (Mac OSX, Linux).
• (All) Nyquist report:
  • Fix for STED channels > 1.
• (All) QMLE:
  • Improve accuracy for Widefield images.
• (E/P) Bleaching Corrector:
  • Fix potential glitch in spinbox causing it to keep looping.
• (E/P) Image Delete:
  • Reinstate old shortcut.

17.10 Release

Highlights

Huygens Professional & Essential

• Deconvolution Express:
  • Visualize raw data and deconvolution results.
  • Select ROIs for deconvolution previews.
  • Customize the sharpness/smoothness for each channel.
  • Enable Deconvolution Express and save the resulting images in a fully automated mode for data loaded through the Image Feeder folder.

• Deconvolution Wizard:
  • A new Deconvolution Preview for ROIs.

• Colocalization Analyzer:
  • ROI drawing tool for masks.
  • Time series plot for colocalization coefficients.

• Hot Pixel Remover:
  • Simplified interface with on-the-fly correction.
  • Improved hot pixel detection algorithm.
  • Import and export hot pixel masks.
  • Correct hot pixels in batch mode.

Huygens Professional

• Multiple Selection of Images:
  • Select several images in the thumbnail overview (Ctlr+Mouse or Shift+Mouse).
  • Many operations can be applied to the selection at once (Decon Express, Export, Save, Fuse, etc).
  • Thumbnails can be reordered.
• Multi-GPU deconvolution:
  • For single images with multiple channels and/or time frames.
  • Available for CMLE, QMLE and GMLE via the Operations Window on Linux.

Minor changes

• (All) Support for unsigned integer data types.
  • Image operations, restoration, visualization, analysis, loading and saving data.
  • All image readers and writers (ICS, HDF5, etc.).
  • Import/Export from/to Leica's LAS X.
  • Due to larger dynamic range fewer cases where scaling is needed.
• (All) QMLE/GMLE:
  • Extend restoration reports.
• (All) CMLE/GMLE:
  • Background estimation: GPU support, more accurate results on very low light backgrounds
• (All) GMLE:
  • Improved handling of images with a Signal to Noise Ratio of around 1.
• (E/P) Colocalization Analyzer:
  • Speed enhancements and RAM reduction for threshold estimators.
  • Save colocalization map in HDF5-format.
• (E/P) Batch Processor:
  • Instead of all GPUs or one GPU, a selection of GPUs to do multi-GPU batch deconvolution can be made.
• (E/P) File Browser:
  • Improved, faster tab completion for the Linux version.
• (E/P) GUI scaling:
  • Allow scaling down for small laptop screens.
• (P) Slicers:
  • Select the default tool for the double-click action (see preferences).

Bug fixes

• (All) CZI reader:
  • Fix negative offset in images with many dimensions (tiles, views, scenes, etc).
• (All) Metamorph ND reader:
  • Fix several cases for ND version 1.0.
• (E/P) Batch Processor:
  • Fix potential communication issue between the Batch Processor and the Compute Engine.
• (T) Fix stalled indexer.
• (E/P) Twin slicer:
  • Improved speed.
  • Fix rotation with MIP and Sum mode.

17.10.0p7 (19th March 2018)

• (All) MultiMIP in Mac OSX for El Capitan or older:
  • Fix tools using the MultiMIP command: Orthogonal Slicer, Cropper, etc.
• (All) HDF5 reader:
  • Fix for foreign HDF5 writers using unsigned integers.
• (All) GMLE:
  • Improve accuracy in cases of extreme low light.

17.10.0p6 (27th February 2018)

• (All) thres command:
  • Fix for unsigned integer images when requesting a binary output.
• (All) DeltaVision reader:
  • Add support for tiled images.
• (All) ND2 reader:
  • Fix for less usual combinations of dimensions.
• (All) TIFF writer:
  • Fix clipped regions when saving to TIFF 16 bit (contrast stretch).
• (All) 'hist' command:
  • Fix name of output image.
• (All) Huygens Modules:
  • Fix potential initialization issue.
• (All) Laplace filter:
  • Add missing support for unsigned integer images.
• (All) Hardware support:
  • Add support for 64 thread CPUs on Windows.
• (E/P) FWHM tool:
  • Fix fitting procedures when on GPU mode.
• (E/P) Stitcher:
  • Fix glitch in queue manager for scenes with 200+ tiles.
• (E/P) Crop window:
  • Fix auto region finding on unsigned integer images.

17.10.0p5 (29th January 2018)

• (All) Support for CUDA 9.1 on Windows.
• (All) Fix error reporting of low level functions which could potentially go silent.
• (All) Fix error in writing parameter states to hdf5 files.
• (All) Fix CPU fallback for the unlikely situation where the GPU deconvolution fails.
• (E/P) Fix updating the contents of the Gallery tool on window resize.
• (E/P) Add a new route to the Huygens Stitcher to adapt the vignetting options without running the image registration again.
• (E/P) Fix potential error when loading an ROI in the Colocalization tool.
• (E/P) Fix initialization problem due to missing DPI preference.
• (E/P) Fix normalization of Manders and Overlap Colocalization maps.
• (E/P) Fix GPU code used in thumbnail generation for multi-time-frame multi-channel images.
• (E/P) Fix that the default value for the signal-to-noise in a per-channel deconvolution template (template editor, Batch Processor) is not a list for all channels any more.

17.10.0p4 (18th December 2017)

• (All) GPU processing:
  • Fix initialization of unknown GPU cards.
• (All) GMLE:
  • Fix occasional variable overflow when on GPU mode.
• (All) Parameter sanitation for Deconvolution:
  • Instead of stopping and raising an error fix impossible NA and objective RI combinations with clamped values. Proceed to deconvolve the image afterwards.
• (P/S/C) Multi GPU Deconvolution.
  • More consequent bleaching correction when splitting a time series over a number of GPU cards.
• (E/P) File Dialog:
  • Fix occasional double entries on the Windows version (Night Theme).
• (E/P) Batch Processor:
  • Fix potential empty result when stabilizing time series after deconvolution in batch mode.
• (E/P) Deconvolution Express:
  • Fix for empty channels.
• (E/P) Fusion Wizard:
  • Fix glitch in rotation estimation.

17.10.0p3 (29th November 2017)

• (E/P) Hot Pixel Remover:
  • Changed default view settings.
• (E/P) Batch Processor:
  • Fix input conversion to floats when requested.
• (E/P/C) Colocalization Analyzer:
  • Fix potential wrong findings in Costes and optimized method.
• (E/P/) Object Stabilizer:
  • Fix occasionally incorrect cropping area.
• (E/P) Export to LAS X 2.0.2:
  • Extend the server side with support for the new unsigned integer type.
• (E/P) Save As:
  • Fix dialog for types other than HDF5 on Windows (day theme only).
• (All) Unsigned Integers:
  • Fix some arithmetic operations that did not promote the input data correctly.

17.10.0p2 (15th November 2017)

• (All) TIFF writer:
  • Fix saving images larger than 2 GB on Windows.
• (E/P) Object Analyzer:
  • Fix sorting table entries based on column criteria.
• (E/P) Save Dialog:
  • Fix TIFF 16 choice which wrongly fell through to the TIFF 8 type.
• (P/C) Multi GPU support:
  • Fix that command-line options to the multi-GPU deconvolution commands that take channelVector-typed arguments cause errors.
• (P) Thumbnail Panel:
  • Faster thumbnail updates when on multiple selection mode.

17.04 Release

Highlights

Huygens Professional & Essential

• SPIM:
  • New Fusion wizard option.
  • Scattering parameters.
• GPU Deconvolution:
  • Full support for the variable PSF mode in CMLE and GMLE.
• Batch Processor:
  • Multi GPU support.
  • Stabilization in Batch mode.
• GUI:
  • Scalable user interface.
  • Day and night themes.
  • Support for 4K monitors
• File readers:
  • Support for Andor TIFF.
  • Support for Metamorph ND.
• New Bleaching Corrector

Minor changes

• (All) CZI reader:
  • Support for JPEG-XR compression.
• (All) ICS reader/writer:
  • Support for parameter states.
  • Support for SPIM parameters.
  • SVI now maintains the open source libics library for reading and writing of ICS data. Since Huygens uses libics the library will be released in sync with Huygens from now on.
• (All) TIFF reader:
  • Support for 32-bit float files.
• (All) LOF/XLIF readers:
  • Support for DSL data.
• (All) OME-TIFF reader:
  • Metadata is loaded.
• (All) GPU support:
  • Made switching to a different GPU device more robust
• (E/P) Huygens - LAS X:
  • Faster communication and data transfers.
• (E/P) Stitcher:
  • Improved support for custom stitching patterns.
  • More visualization controls.
  • A new MIP visualization mode.
  • Better performance and less memory consumption.
  • Disable background estimation and bleaching correction for the tile deconvolution.
• (E/P) Batch Processor:
  • Improved GUI.
  • Support for loading LIF files with multiple levels of sub-images.
• (E/P) Improved icons.
• (P) Improved image convert window.
• (E/P) Crosstalk corrector:
  • Reduce noise option
  • Correction is now energy conservative.
• (E/P) Tab completion is available in the open file window on Linux.
• (C) SFP renderer:
  • Threshold data by Otsu's method for rendering raw and deconvolved images.

Bug fixes

• (All) CZI reader:
  • Fix 'Scale if necessary'.
• (All) LIF reader:
  • Several fixes.
• (All) ND2 reader:
  • Several fixes.
• (All) Background estimation:
  • Fix background calculation on the CPU for floating-point images containing integer values.
• (E/P) Drag & Drop:
  • Fix Windows and Linux distributions.
• (E/P) Communication with Leica's LAS X software:
  • Fix floating licenses.
• (E/P) Histograms:
  • Fix potential bug in the calculation of 5+ channel histograms.

17.04.1p2 (20th October 2017)

• (All) Split channels:
  • Fix regression that caused the split command to ignore channel meta data.

17.04.1p1 (18th October 2017)

• (All) Coverslip Editor:
  • Fix wrap around effect on deconvolution for negative coverslip positions.
• (All) Split channels:
  • Fix potential error in the confidence levels of the extracted channels.
• (E/P) HyVolution:
  • Fix deconvolution of STED 3X channels with very short PSFs previously failing at the Z stabilization step.

17.04.1p0 (2nd October 2017)

• (All) HDF5 files:
  • Fix occasional hard error while loading images.
• (All) ND2 files:
  • Fix occasional hard error while loading images.
• (All) Metamorph ND files:
  • Fix loading old versions.
• (All) GPU deconvolution:
  • Fix a problem in the fall-back from the GPU to the CPU in case the GPU encounters a problem due to e.g. lack of available memory.
• (All) Windows:
  • Fix initialization of GPU device(s) when using CUDA 9.
• (E/P) File Series Tool:
  • Fix occasional error when the files names have too many patterns.
• (E/P) Fusion Wizard:
  • Fix deconvolution and microscopic parameters template buttons.

17.04.0p9 (15th August 2017)

• (All) GPU processing
  • Use a sufficiently large string to report the names of all GPU cards.
• (E/P) Decon Express:
  • More consistent SNR reports.
• (E/P) Colocalization Analyzer:
  • Fix inaccuracies in computation of Pearson coefficient with a mask image.
• (E/P) Cross-talk Corrector:
  • Fix potential low level error.
• (E/P) Chromatic Aberration Corrector:
  • Fix interpretation of templates where there are missing values. This fix also affects the Batch Processor where the corresponding job could fail due to the missing value.
  • Editing the table is now slightly easier. Allow for empty cells.
• (E/P) Batch Processor:
  • Add a new cascading menu to set the input conversion format for integer-typed input images to either int (the default) or float.
  • Fix interpretation of no stages in Metamorph .nd files.
• (E/P) Stitcher:
  • Fix regression introduced in previous patch which rendered the quick launch button useless.
• (P) Enable/Disable 'Split' entry in 'Tools' menu depending on context.

17.04.0p8 (18th July 2017)

• (All) Compute Engine:
  • Fix unresponsive 'genpsfExpl' command.
  • Fix GPU initialization that would disable the GPU as a whole with more than 3 GPU devices present.
• (All) ICS files:
  • Limit the number of channels to 32.
• (All) HDF5 files:
  • Fix a crash and convert it into a regular read error when reading a certain HDF5 file (with invalid data).
  • Fix a crash on reading scaling data from a multi-channel HDF5 file.
• (All) OME reader:
  • Report an error in case of an invalid number of channels or an invalid channel number.
• (All) LIF reader:
  • Fix SPIM excitation mode.
• (E/P) Stitcher:
  • Fix neglected channels in TIFF series.
  • Fix layout optimization of mosaics containing very noise as well as signal-rich tiles.
  • Fix occasional 1-pixel wide artifacts at the borders.
• (E/P) SFP Renderer:
  • Fix table switch.
• (E/P) Deconvolution Wizard and Deconvolution Express:
  • Fix occasional glitches in report area.

17.04.0p7 (30th June 2017)

• (E/P) Twin Slicer:
  • Fix focus issue of the contrast window in Windows.
• (E/P) Batch Processor:
  • Fix incorrect undersampled highlighting in microscopic templates.
  • Fix saving error of files containing unsupported path symbols (e.g. colon symbol) on Windows.
  • Fix missing update of the screen after loading a batch job list from file (new list was not shown in some cases).
• (E) Fusion Wizard:
  • The tool is now available in Huygens Essential.
• (All) Deconvolution:
  • Fix SNR multichannel report which failed to concatenate the single channel strings.
  • Fix small memory leak in the GPU version of GMLE.
  • More accurate background estimation of extremely low signal images.
• (All) LIF files:
  • Read transmission channels as brightfield.
• (All) HDF5 files:
  • Report when the file has been generated with a newer Huygens version.
• (All) Metamorph ND files:
  • Fix case where there's only 1 position in a multi stage file.

17.04.0p6 (9th June 2017)

• Fix occasionally incorrect background report.
• Addition to preference window; the user can change what happens after a double clicking on a thumbnail in Huygens Professional: Open a slicer, twin slicer, MIP renderer or orthoslicer.

17.04.0p5 (1st June 2017)

• Slightly smaller font for the Tcl shell.
• Microscopic Parameter Editor: fix reported Nyquist rate for SPIM which did not take excitation mode into account.

17.04.0p4 (24th May 2017)

• Fix error on closing the preferences window while the GUI was scaling.
• Remove automatic DPI scaling which gives errors on OSX.

17.04.0p3 (19th May 2017)

• Fix 'Experimental Presets' in Object Analyzer.

16.10 Release

Highlights

Huygens Professional & Essential

• Automated, one button deconvolution via the new "Deconvolution Express" option:
  • A new method to do "unsupervised deconvolution" allows the user to get a quick, effortless deconvolution result, requiring no further user action.
  • Via right-clik on the image or via the main menu -> Deconvolution -> Deconvolution Express.
  • If needed, the user can fine-tune the method used for unsupervised deconvolution. Deconvolution Express offers a choice of fast, standard, conservative or aggressive methods.
  • Huygens can estimate several parameters such as the SNR based on image meta data and image structure.
• Deconvolution:
  • GPU support for the most commonly used type of background estimation: the 'lowest' background mode.
  • Improved adaptation of brick layout to the available GPU memory
• SPIM:
  • New sheet types now include Multi View 'MuVi', Bessel beam, two-photon Bessel beam.
  • Improved strip-like layout of bricks, adapted to the GPU memory if a GPU is available.
• Object Stabilizer:
  • New and improved interface for the Object Stabilizer.
  • GPU support for cross correlation stabilization method.
• Chromatic Aberration Corrector:
  • GPU support for the shift correction method.
• GPU acceleration:
  • Support for CUDA toolkit 8.0.
• New Huygens Server for communicating with Leica's LAS X software:
  • Possibility to exchange data between Huygens and LAS X.
  • Specify your LASX version in the Huygens preferences window.
  • Huygens can deconvolve imported images automatically by using the infrastructure of the new "Deconvolution Express".

Minor changes

• (All) Background estimation:
  • Improved pre-filtering of the image when calculating the "WF" mode.
• (All) GMLE deconvolution:
  • improved handling of very shallow or 2D images.
• (All) Windows installer:
  • Warn the user if Huygens is running when there's a request for uninstalling or reinstalling the software.
• (All) GUI:
  • Default thumbnails size is now chosen according to the monitor size.
  • The numerical keypad's "enter" key behaves in the same way as the main keyboard's "enter"/"return" key on Linux and Mac.
  • The "enter" key invokes the selected option instead of the default option in questions with multiple answers.
• (All) CZI reader:
  • Add support for cases where the ZISRAWDIRECTORY segment is missing.
  • Fix case where the pinhole of one of the channels is missing.
  • Update internal magnification of LSM800.
• (E/P) Colocalization Analyzer:
  • Extra column in the results tab to show the contribution of each object to the total coloc coefficient.
  • Background value can be set to 0.
  • Improved return value handling in Tcl coloc command.
• (E/P) Stitcher:
  • Improve support for custom stitching patterns.
  • Allow 0% tile overlap.
• (E/P) Communication with Leica's LAS X software:
  • Show 3 decimal digits at most in scaling factors.
  • Add XML headers to Huygens attachments.
• (E/P) Object Analyzer:
  • Improved performance.
• (E/P) Track Analyzer:
  • More intuitive names, labels and help texts.
• (E/P) GPU Window:
  • Added the possibility of changing GPU card.
  • GPU status is now linked to on/off preference without waiting.
• (E/P) Twin Slicer:
  • Frame number and time (seconds) are now shown by default on time series.

Bug fixes

• (E/P) Communication with Leica's LAS X software:
  • Opening a LIF sub image in Huygens and exporting to Leica results now in more precise meta data.
  • Restore the use of full 16-bits range when exporting to Leica which was briefly disabled in the 16.05.1X version.
• (E/P) Batch Processor:
  • Fix slow behaviour when listing many files or deconvolution jobs.
• (E/P) SFP Renderer:
  • Fix several scene inconsistencies.
  • Fix a crash on an image with very many pixels in a single slice.
  • Fix the re-centering of the image after the windows is resized.
• (E/P) MIP Renderer:
  • Fix the re-centering of the image after the windows is resized.
• (E/P) File Series tool:
  • Fix launching the Stitcher with only 2 tiles.
• (E/P) Stitcher:
  • Fix displaying only 1 channel when opening file series.
  • Fix hidden brightness tool with multi channel images.
• (E/P) Fix potential issue on opening an internet browser from hypertext in Huygens.
• (All) Histogram:
  • Fix marginal case where the count can be off by 1.

16.10.1p4 (3rd May 2017)

• Fix regression in Operations Window where the CMLE command did not show input fields for the SNR parameter.
• Fix regression when changing the acquisition pattern in the stitcher.
• Fix regression in HuCore and Batch Processor: some parameters could be loaded from the meta data unnecessarily.
• Fix ND2 3D time-series read as one big z-stack.
• Fix Nyquist estimation of STED and SPIM images in the Parameter Editor.
• Improve distance accuracy of tracks in Tracker Analyzer.

16.10.1p3 (16th March 2017)

• Fix multiple tile selection in the stitcher (Shift + Left mouse click).
• Fix differences between OP and BP/DW runs due to a missing 'varPsf' option in the deconvolution templates.
• Fix wrong acquisition pattern tile order when adjusted in stitcher. It is now possible to adjust the acquisition pattern overlap without touching the pattern.
• Fix error in stabilize scripting command.
• Improve OME Tiff handling of missing XML tags.
• Fix incorrect handling of microscopic template in the Stitcher.
• Fix incorrect number of CUDA cores for NVIDIA's Pascal generation.
• Show correct scaling factors of CZI images where the factors were not reported.
• Improve reading of chunk dimensions in VSI reader.
• Fix regression in HuCore where the parameter confidence levels got replaced by the template parser.
• Fix conversion of Zeiss light sheet thickness.

16.10.1p2 (22nd February 2017)

• Improve performance of data transfers between LAS X and Huygens.
• Fix (potential) bug in the calculation of 5+ channel histograms.
• Fix (potential) incorrect interpretation of XML files in Stitcher. Improve memory management. Faster flipping and swapping.
• Support added for Metamorph ND files version 1.0 in the Full file reader option
• Add scaling factors to HDF5 file reader / writer.

16.10.1p1 (2nd February 2017)

• Fix saving 2D images as JPEG for HRM tools.
• Fix ND2 3D time-series read as one big z-stack.
• Fix floating licenses for HyVolution.

16.10.1p0 (24th January 2017)

• Fix 'drag&drop' on Linux and Windows.
• Support for Multi GPU environments in HuCore/HRM.
• Support for Metamorph ND files (version 2).
• Update ome-tiff reader for importing more meta data parameters.
• Fix error in the Windows version of the CZI reader.
• Fix 'scale if necessary' of 16 bit unsigned integers in CZI reader. Add check for overlap between emission and detection wavelengths.
• Fix incorrect interpretation of confocal/STED channels in some LIF files.
• Let HuCore determine a more suitable threshold when creating top SFP's.

16.10.0p9 (12th January 2017)

• Fix potential error in Decon Express when dealing with ICS files.
• Fix Batch Processor: divide by zero
• Fix manual vignetting in Stitcher.
• Strip '.nd2' suffix from Nikon image names.
• Fix silent truncation of data if more than 4 GB of data is transferred from, or sometimes to, the GPU in a single copy command.
• Fix incorrect dimensions in VSI file exported from CellSens.

16.10.0p8 (12th December 2016)

• Many improvements in the Stitcher: control panel, better support for multi channel XMLs, more intuitive deconvolution, and more.
• Multi GPU Batch Processor: run jobs in parallel on different GPU cards (requires server option).
• Prevent problems by disallowing to enable/disable the GPU system or to switch the current GPU device while a computation is in progress.

16.10.0p7 (22nd November 2016)

• Fix potential crash in GPU deconvolution.
• Fix error in Object Stabilizer when changing time frame before displacements are computed.
• Fix hidden 'export to LAS X' when there's an 'H' flag and no 'L' flag in the license.

16.10.0p4 (15th November 2016)

• Fixes when switching GPU devices: i) Prevent resource leaks; ii) Prevent cached FFT plans from being used on the wrong GPU device.
• Skip the batch chromatic aberration correction if all vectors are 0.
• Fix editing chromatic aberration correction vectors in batch mode.
• Fix 'Check for updates' button in 'Help' menu.
• Support reading the SPIM excitation direction from Leica LIF files.

16.10.0p3 (2nd November 2016)

• Fix for RPM packages using CUDA versions older than 8.0.
• Fix for Windows packages using CUDA 7.5.
• Report frame scaling factors in Decon Express, Decon Wizard and HyVolution.
• Close Decon Express windows upon removing the source images.

16.05 Release

Highlights

Huygens Professional & Essential

• Stitcher:
  • Now available in Huygens Essential as well as in Professional.
  • GPU support.
  • Basic support for custom stitching patterns.
  • Support for TIFF based file series.
• Cropper:
  • Improved performance.
  • Efficient handling of large images.
• Twin Slicer:
  • New MIP and Sum projection modes.
  • New Contrast Editor for customized channel visualization; for reporting gamma factors and exporting LUTs.
• GPU status window: improved diagnostics for trouble shooting
• SPIM/Light Sheet Deconvolution:
  • New SPIM Excitation Mode settings (see SPIMDeconvolution)

Huygens Professional

• Plugin system:
  • The system for creating loadable plugins has been rewritten to be more simple, and to support Windows (see Huygens Modules).

Minor changes

• (All) In Tiff reader:
  • Add support for JPEG compression.
• (All) In LSM reader:
  • Add LSM 800.
• (All) In CZI reader:
  • Better handling of multiphoton parameters.
• (All) in VSI reader:
  • Update to latest file specification.
• (All) In Imaris writer:
  • Improved handling of single-slice 3D images.
• (All) In LIF reader:
  • Extract and save the sub image meta data from a LIF collection.
• (All) On Windows, add support for NUMA processors including all their cores.
• (All) Workaround for NVIDIA's issue where no processing of specific image geometries is accepted at all by the GPU card.
• (E/P) Surface Renderer:
  • Add the same render buttons as in the MIP and SFP renderers.
• (E/P) Chromatic Aberration Corrector:
  • Better performance and more accurate scale and rotation.
• (E/P) Othogonal Slicer:
  • Remove deprecated version. Enable newest version only.
• (E/P) MIP renderer and SFP volume renderer
  • Changed the channel selector which enables to switch off channels.
• (E/P) Deconvolution Wizard:
  • Fix hard error on clicking the 'Cancel' button during deconvolution.
  • Add 'GMLE' algorithm choice to confocal data sets. Skip it on 2D data.
• (E/P) PSF distiller:
  • Support for SPIM/light-sheet microscopes.
• (E/P) Object Analyzer:
  • Speed enhancements when analyzing large number of objects.
• (E/P) Object Stabilizer and Object Tracker:
  • Fix stage-dependent 3D slicing.
• (E/P) Significant speed enhancement for the median filter on byte and integer image types.
• (E/P) Improved error reporting of GPU-related problems.
• (P) Performance Wizard:
  • Limit number of trial threads to the CPU. Skip the GPU where all threads are used.
  • Try the licensed microscopy types only.
• (E) Add Leica LASX export button.
• (C) Add on-demand GPU option to deconvolution templates.

Bug fixes

• (All) In ICS reader:
  • On Windows: reading and writing data sets that are larger than 2GB.
  • On Windows: allow the use of extended characters (such as é) in file and directory names.
  • Several fixes for ICS related crashes and for failures to read/write ICS files.
• (All) In LIF reader:
  • Fix for reading data generated by Leica´s Live Data mode module.
• (All) In ND2 reader:
  • Fix hard error on specific data.
  • Fix potential memory corruption.
• (All) In Ome writer:
  • Large images are written correctly.
• (All) MultiMIP yields more consistent results when single-slice images are used.
• (All) Delayed event handling has been improved such that potential problems are prevented when Huygens is closed.
• (All) Fix regression in histogram command.
• (All) On Windows, fix potentially incorrect System IDs which encode 0 cores and lead to astray image processing.
• (E/P) In Batch Processor:
  • Fix interpretation of 'varPsf' option.
• (E/P) In GPU QMLE, fix display of deconvolved result.
• (E/P) In Plot Profile Tool:
  • Fix far from centered default profile.
• (E/P) In Plot Flux Tool:
  • Fix grey color palette.
• (E/P) In File Series Tool:
  • Fix error when clicking 'Load Selection' on just one file.
• (E/P) In Stitcher:
  • Fix zoom jumps.
• (E/P) In MIP renderer:
  • Fix incorrect verbosity level leading to multiple questions.
• (E/P) in Surface Renderer:
  • Fix rendering artifacts on extreme large zoom factors.
  • Fix default movie preset.
• (E/P) Fix incorrect busy state on opening an unsupported file.
• (E/P) Stabilizer: fix crash on very unstable images.
• (T) Indexer logs from Titan do not consume as much disk space anymore.

15.10 Release

Highlights

• GPU acceleration of all major deconvolution algorithms. More info here. Installation instructions can be found here.
• Improved deconvolution of SPIM data.
• New LIF reader (Leica) is faster, uses much less memory, and reads recently introduced microscopic parameters.
• Improved floating license option More info here

Huygens Professional & Essential

• Object Tracker and Object Stabilizer: new embedded Orthogonal Slicer.
• MIP Renderer:
  • Support for complex type images.
  • Support for much larger image volumes.
  • Performance and quality improvements in the high quality mode.

Huygens Professional

• Stitcher:
  • Support for TIFF files and XML layouts.
  • New "Flip & Swap" for changing the layout orientation.

Huygens Titan

• Streamlined main window:
  • First usage help page.
  • Clear distinction between Projects and Annotations.
• Additional Tabs:
  • To monitor Titan's activity.
  • View the state of removable drives.
• Improved responsivity under load.

Minor changes

• (All) In deconvolution algorithms:
  • Report bleaching factors per slice and per frame.
• (All) In LSM reader:
  • Add LSM 780.
• (All) In HDF5 reader/writer:
  • Add support for SPIM parameters.
• (All) In ICS reader/writer:
  • Add support for STED parameters.
  • Add support for channels with different microscope types.
• (All) in Compute Engine:
  • Faster opening of all large files.
  • Performance increase in stat command for byte images.
  • Large performance increase in range command, especially for byte images.
  • Performance increase in hist (histogram) command.
  • Performance increase in cs (copy and stretch) command.
  • Add support in label function for 2D binary images.
• (E/P) In Parameter Editor:
  • Add embedding media Vectashield and Mowiol.
• (E/P) In MIP Renderer:
  • Automatically renders when zoomed with the mouse wheel.
  • Higher resolution for the quick mode engaged while dragging.
• (E/P) In Surface Renderer:
  • More efficient memory usage.
  • Increased height to prevent occlusion of widgets in Movie Maker mode.
• (E/P) in Renderers:
  • Tilt can now be 360 degrees for all renderers.
• (All) Improved robustness of Floating License requests.
• (All) Improved reading of Z-stacks and T-stacks in ND2 files.

Bug fixes

• (All) in Compute Engine:
  • borderFill for 2D images would clear image.
• (E/P) In Chromatic Aberration Corrector:
  • Fix estimation of rotation between channels.
• (E/P) In Object Analyzer:
  • Seed and threshold manipulation with keyboard now also added to history.
• (E/P) In Colocalization Analyzer:
  • Don't allocate too much RAM when computing coefficients with a mask.
• (E/P) In SFP Renderer:
  • Fix potential overflow on the number of voxels.
• (E/P) In MIP Renderer:
  • Show the displayed frame correctly:
• (E/P) In Surface Renderer / Object Analyzer:
  • Fix display of binary images.
  • Fix potential artifacts in integer images when the selected threshold is also an integer.
• (E/P) In Object Analyzer:
  • Fix position of loaded ROI.
• (E/P) In PSF Distiller:
  • Fix potential empty result.
• (E/P) In Movie Maker:
  • Fix high quality rendering for the MIP and SFP renderers.
  • Fix the preview when the transformation includes a shift.
  • More precise zooming interpolation (fixed stuttering).
• (All) Fix several small memory leaks in file readers.

15.05 Release

Highlights

• New CMLE and TM deconvolution algorithms on GPU (on request).
  • Can use brick wise deconvolution to accommodate limited GPU memory.
• New optical option for light sheet (SPIM) data sets (on request).
  • Computation of SPIM PSFs.
  • Adapted brick layer to deconvolve areas of the image where the light sheet is thicker with different PSFs

All Huygens Products (incl. Titan)

• New reader for VSI files.
• New reader for JPEG files.
• Experimental new reader for Leica LOF and XLIF files.
• Floating licenses

Huygens Professional & Essential

• Chromatic Aberration Corrector
  • Replaces the Chromatic Shift Corrector.
  • New improved GUI for better workflow.
  • New correction method which also corrects for rotation and scaling.
• Deconvolution wizard
  • Improved workflow for template execution.
  • More informative entry page
• Redesigned Parameter Editor
  • Includes parameter editors embedded in the Batch Processor, Distiller, and Operations Window.
• New API to exchange images between Huygens and other softwares (available on request).

Huygens Professional

• Stitching tool
  • Support for TIFF tiles.
  • New options for automatic vignetting correction.
  • Improved performance.
  • More accurate stitching results.
• SPIM support
• Convert deconvolution job in Operations Window to template via the Template Editor
• Extended Tikhonov-Miller deconvolution supporting brick-wise computations and automatic generation of theoretical PSFs.

Huygens Titan

• Increased freeware indexing limit from 10GB to 200GB
• Support for JPEGs in image indexer and search results.
• New searches on:
  • Nyquist compliant images
  • Targets for stabilization and colocalization
  • Image resolution
• Search improvements
  • Filename search using and/or on multiple keywords
• Improved activity monitor
• Preference to set directory for temporary files (thumbnails/database).

Minor changes

• (All) Improved error messages for img sub commands.
• (T) In Huygens Titan:
  • Removed redundant version check that slightly impacted indexing performance.
  • Improved error handling when a thumbnail could not be generated due to the memory limit. An 'image too big for now' message is now displayed instead of a generic error message.
  • Notify that an image is not yet indexed in the image metadata area instead of waiting.
• (E/P) In Deconvolution Wizard:
  • New welcome screen presents an overview of important optical parameters.
  • Removed unused iteration field for qmle algorithm.
  • Improved workflow for the template save stage.
  • Reduced processing time when executing templates.
  • Enabled 'estimate psf' button for STED Channels when using a theoretical PSF.
  • Added "Autocrop" to the template functionality.
• (E/P) In Gallery:
  • Border is now dependent on image dimensions instead of fixed.
  • Display a black border when #000000 is selected as border color.
• (E/P) In Template Editor:
  • Better layout (some widgets were obscured).
• (E/P) In Twin Slicer:
  • Reset view now also resets contrast stretch.
• (E/P) In Ortho Slicer:
  • Tool can now be closed via the File menu.

Bug fixes

• (All) In VSI reader:
  • Long file names could be truncated, preventing the files from being opened.
• (All) In ND2 reader:
  • Long file names could be truncated, preventing the files from being opened.
• (All) In CZI reader:
  • Huge CZI files could not be loaded in Windows.
• (All) In "img preOpen" command:
  • Resources could be leaked.
• (E/P) In Deconvolution Wizard:
  • Some templates would not load PSF.
  • PSF could only be loaded once.
• (E/P) When using templates the Twin Slicer could not be launched at the last wizard stage.
• (E/P) In Object Analyzer:
  • ROI could be incorrectly shifted on loading from file.
• (E/P) In Gallery:
  • Clicking on a slice would not show the slice in the detailed view.
• (E/P) In Colocalization Analyzer:
  • The analysis could be carried out on a padded image.
• (E/P) In Surface Renderer:
  • A crash could occur when the MIP and slicer were used from a specific viewpoint.
• (E/P) In PSF Distiller:
  • The wizard would get into an undefined state if a channel didn't contain any beads.
• (E/P) In Performance Wizard:
  • The tuning would not be aborted after closing the window.
  • The wizard could not be restarted after closing it from specific window controls.
  • A run would not get started without a confocal flag.
• (E/P) In Batch Processor:
  • File series where the 'h' of 'Ch' was missing would not be recognized.

14.10 Release (Fall 2014)

Summary

• New tool: Gallery, view all slices of an image in a tiled view.
• New functionality: Image feeder, a sort of Dropbox for Huygens.
• Updated tool: Hot pixel remover, analyze and remove the hot pixels from a raw image.
• New tool: Performance tuner, tune the amount of cores Huygens uses for image processing.

All Huygens Products

• Performance optimization of the CMLE deconvolution algorithm and several low level image processing algorithms.
• GMLE deconvolution: Improved handling of very noisy images, in especially STED and confocal data.
• Deconvolution reports per channel and frame on the applied background correction.
• Reader for the new Olympus VSI format.

Huygens Titan

• Titan uses relaxed criteria when opening very large LIF files. All LIF files are now opened during initial indexing so that Titan knowns the structure of the LIF file immediately.
• Added 'placeholder' images for very large images that Titan doesn't open during initial indexing. This allows the user to force Titan to generate a thumbnail immediately, even when the current memory limit wouldn't allow the thumbnail generation.
• Enhanced the way Titan detects series. Titan should now detect even more series, which greatly improves usability and performance.
• Improved indexing of container formats. Titan now tries to detect the image size of the subimage. This greatly increases the number of sub-images that Titan indexes automatically.

Huygens Professional

• Stitcher:
  • Added automatic vignetting correction.
  • Improved overall performance and memory usage.
  • Corrected orientation of tiled LIF sub images.

Huygens Essential

• Activated import/export option with LAS X software.

Minor changes

• (All) Add support for tiled OME-TIFF files.
• (All) Renamed term subBrick as varPsf which is more accurate to describe what this option implies.
• (All) Changed default value of STED saturation factor from 40 to 30 in 'genPsfExpl' command.
• (E/P) Removed option 'Save as HDF5' from Deconvolution Wizard thumbnails.
• (E/P) In Deconvolution Wizard do not load the Twin Slicer preferences but use the default ones instead.
• (P) In Stitcher Wizard do not load the Twin Slicer preferences but use the default ones instead.

Bug fixes

• (All) In license mechanism: string licenses with no extra flags did not get recognized.
• (All) In LSM file reader: Emission wavelength was not estimated accurately for low pass and short pass filters.
• (E/P/C) In Batch processor and HuCore jobs: the sampling distances were not properly loaded from the templates, instead the metadata values were used.
• (P/S/C) In ICS file writer: data compression was not enabled as intended.
• (E/P) In Batch Processor: the selected sub image did not get processed. Instead, a different sub image from the same data set was deconvolved.
• (E/P) In Stabilizer: a license check for Object Analyzer was not needed.
• (E/P) In Stabilizer: the outliers slider did not behave as intended.
• (E/P) In Colocalization Analyzer: Huygens could fail to launch the tool.
• (E/P) In SFP renderer: the scene's aspect ratio and perspective could be wrong depending on the image geometry.
• (E/P) In thumbnails: a license check meant for Tracker checked on a different option instead.
• (E/P) In PSF Distiller: an error could be thrown when closing the tool before reaching the last workflow stage.
• (P) In Stitcher: the normalization of the flat-field image could fail.
• (P) In Stitcher: the mosaic corners could look a bit too rounded.
• (T) Search on filename instead of image name in the advanced search.
• (T) Fixed bug where images with very large metadata fields where not loaded correctly.
• (T) Fixed bug where searching of path doesn't work in the advanced search.
• (T) Increased size of annotation comment field.
• (T) Fixed error where Titan would not go to the correct directory when select 'Find in library tree' in the advanced search tab.

14.06 Release (Spring 2014)

Summary

• New product Huygens Titan.
• New stitching option for Huygens Professional.
• New deconvolution algorithm: GMLE.
• New sub brick wise deconvolution.

All Huygens Products New way to handle shape changing PSFs The shape of PSFs suffering from spherical aberration due to refractive index mismatch is dependent of their depth position in the specimen. Previously this was solved by splitting the image into 'bricks', each with their own PSF. Though efficient, this could give rise to difficult to avoid gluing artifacts. With the new 'sub-brick' method, the Fast Fourier Transform (FFT) based convolution operations which are the heart of all deconvolution algorithms, are replaced by multiple FFTs, each with different PSFs. This new technique is available for the CMLE, QMLE and the new GMLE deconvolution algorithms. GMLE The GMLE algorithm is based on the Maximum a Posteriori probability estimation with Good's roughness regularization. It is related to our workhorse CMLE algorithm, but has rapid convergence like the QMLE algorithm. Using the newly developed sub-brick scheme, it is able to deal with shape changing PSFs without resorting to brick-wise processing. GMLE is by default available for STED data. To use GMLE in the Deconvolution wizard for other imaging modalities 'Expert mode' needs to be switched on.

New product Huygens Titan

• Indexes all your microscopic images. Titan is a local indexer; you don't need to upload and convert your files to a centralized database, the images and the database stay on your personal computer.
• Offline index: index your external hard disks and disconnect them. If you want to open an indexed image Titan will tell you on which external hard disk the image is stored.
• Tag images with texts and group them into Projects.
• Search in your image database on metadata or annotations.
• Quickly inspect your image in 5D using the Lightbox image viewer.
• Open images directly in Huygens Essential or Huygens Professional for deconvolution and analysis.

Huygens Professional - Stitching Option

• New, fully automatized stitching option.
• The stitched scene can be deconvolved while the scene pieces are put together.
• Vignetting & shading correction is possible upon providing flat field references.
• Support for CZI and LIF file formats containing information on tile offsets. Support for other formats is underway.

(E/P/C) Batch Processing

• New 'Autocrop' option allows for conservative cropping of images in batch mode.

Minor changes

• (All) Support for two level nesting LIF files.
• (All) The 'preOpen' command returns more information when working with LIF files.
• (E/P) The STED parameters will be displayed even if no STED license is present.
• (E/P) Replace ":" with "_" in Deconvolution Wizard results to be more compliant with OS file managers.
• (E/P) Add LSM 780 to LSM-specific dialog.
• (All) Skip the STED Z Stabilization (though not the UI option) if the dataset differs too much from vortex STED.
• (All) Minimize the output of the STED Z Stabilization.
• (E/P) Change order of 'Skip' and 'Correct' buttons in Z drift stage (Deconvolution Wizard).
• (C) Add format reports of STED parameters as required by HRM 3.1.
• (E/P) Adapt texts in Chromatic Shift help, dialogs and reports (Batch Processor only).
• (All) 'huOpt getFormatInfo' includes the ND2 file format.
• (E/P) Parameter "Object size" has been renamed as "Penetration Depth" in the SFP renderer.
• (All) New installer for Mac OS X. Installer removes deprecated binaries that depend on the Aqua toolkit.

Bug fixes

• (All) Saving with compression was skipped for the target format ics/ids.
• (E/P) Fix wrong import of the STED 3D parameter when loading old templates in which STED 3D was not present. The default value was wrongly set to 100% whereas it should be 0%.
• (E/P) Report STED parameters in optical tab.
• (All) Fix empty result produced by STED deconvolution + measured PSFs.
• (S) Fix unwanted flip of Y coordinates introduced by Huygens on images provided by MBF Bioscience's clients: 'Stereo Investigator' and 'Neurolucida'.
• (P) Fix icon selector which failed to show when the Huygens preferences contained stitcher entries.
• (E/P/C) Fix bug in the 'huOpt' commands which caused the Batch Processor to stall with STED 3D datasets + Stabilization.
• (E/P) Fix thumbnail menu which (wrongly) grayed out the MIP entry in Freeware mode.
• (All) Fix ZVI reader which failed to read RGB24 and RGB48 types.
• (All) Fix memory leaks in STED deconvolution (sub brick mode).
• (All) Fix in-place and not-in-place stabilization of STED time series (stabilizer tool and "stabilize" command).
• (All) Fix error in STED deconvolution ocurring when NA > R.I. (lens).
• (E/P) Fix Twin Slicer time swing.
• (All) Fix wrong calculation (factor 2) in backprojected pinhole radius (LIF data only).
• (E/P) Fix a reporting problem in the Batch Processor which hid many statements when the license included the STED + Leica features.
• (All) Fix memory leaks in the LIF reader.
• (E/P) Fix 'Done' button which the Deconvolution Wizard missed in a particular (seldom used) route.
• (E/P) Fix bug in MIP renderer happening when the user chose "Customized Render Size" but provided no customized size.
• (E/P) Fix wrong background colors in Parameter Editor (Windows Vista and higher).
• (E/P) Fix brick mode which failed to show the deconvolved results in the corresponding thumbnail (Operations Window and Tcl Shell only).
• (All) Fix 'unspecified' microscope type when opening OME files.
• (E/P) Fix timeout issue in Deconvolution template editor. The value was not properly saved for all channels.
• (E/P) Fix error where Object Analysis results in Colocalization Analyzer could not be saved.

4.5 Release (Fall 2013)

Summary

• New and improved Orthogonal Slicer (E/P)
• New Nikon ND2 file importer (E/P)
• Improved PSF FWHM (Full Width Half Maximum) Analysis tool (E/P)
• Chromatic Shift Correction made available in Batch Processor (E/P)
• STED option extended for Leica STED 3X.
• Improved and extended LIF file reader (E/P)
• Huygens <-> Leica LAS AF data exchange possibility (E/P)
• Significant performance and stability improvement for X11 versions of Mac OS 10.7, 10.8, and 10.9 (see also here)

PSF FWHM Estimator

• (E/P) A tool is added to the PSF distiller to analyse a newly distilled PSF by checking the FWHM of the PSF in all three dimensions.
• (E/P) Gauss, Lorentzian, Voight and Pearson7 curve fitters have been added.
• (P) If you have the PSF distiller in your license, the Huygens Professional Analysis menu activates the PSF FWHM Estimator item, to estimate the FWHM (HIW) of already distilled PSFs.

(E/P) Twin Slicer

• Animation buttons are added to the Twin Slicer next to the time slicers and z slicer. The Animate tab can be used to adjust the number of frames per second.
• You can reset all viewing parameters to default values in the Twin Slicer, which can be found under View > "Reset view to default".
• The time-frame sliders in the Twin Slicer now move with discrete steps.
• Stretch the contrast per screen or globally.

(E/P) Nikon ND2 file importer (Now in Essential and Professional. Expected to be in the HRM per January 2014).

• This file importer allows Huygens to read Nikon ND2 images. This importer is still considered experimental as metadata extraction is not always read in correctly with certain ND2 file dimensions. We encourage our users to send us their ND2 files and feedback so we can further improve this reader.

(E/P) Ortho Slicer

• A NEW and improved ortho slicer.
• More intuitive and easy to use tool.
• Place the slicer anywhere you want and visualize the slices in all three direction
• New slicing modes MIP and SUM.
• Cut thick slices by setting a span
• Show the corresponding histogram of the selected time frame.
• Stretch the contrast per screen or globally.

(E/P) STED option

• Perform deconvolution with images from the latest Leica STED 3X system. STED 3X deconvolution uses a new depth-dependent PSF.

(E/P) Batch Processor

• The Chromatic Shift Correction is included in the processing workflow of the Batch Processor.

(E/P) Leica software compatibility

• Improved and extended the LIF XML microscopic parameters parser.
• Expected in January: Huygens <-> Leica LAS AF data exchange possibility.

(E/P) Deconvolution Wizard

• Loading deconvolution templates with Chromatic Shift tasks allows the user to choose for chromatic shift correction after deconvolving the image.

(E/P) Colocalization Analyzer

• Mask visualization in the Colocalization Analyzer.
• Extended the Colocalization Analyzer to also show the Colocalization Map for 2D images.

(E/P) Object Analyzer

• The Object Analyzer is extended with a Ripley k-function:
  • When the distance towards the anchor is calculated (a.CMCM), you can request for the clustering around this specific object by right click on the column and select "Ripley k-function".
  • If you want a full cluster analysis (distances of all objects to all objects) the "Full Ripley k-function" shows the k-function of all distances.

(E/P) Object Tracker

• When slicing through time, tracks in the Track Analyzer now follow the objects for a more intuitive feel.

Minor changes

• (All) Improvements in the interpretation of CZI meta data.
• (All) Increased the limit of slices that Huygens can handle in a single dataset from 5000 to 7000 slices.
• (All) When opening LIF files their XML section will be stored for future reference. This information will be attached to the image when it's saved as HDF5 in Huygens.
• (All) When opening OME TIFF/OME XML files the meta data provided as XML will be stored for future reference. This information will be attached to the image when it's saved as HDF5 in Huygens.
• (All) Better pixel conversion when loading unsigned integer CZI images.
• (All) Added joining and splitting, and statistics and histograms now possible with binary images.
• (P/S/C) The 'stat' command now also returns the minimum non zero.
• (P/S/C) Added a command 'solvePGauss' to solve linear systems by using the Gauss-Jordan method. The matrix coefficients must be provided as pixels of a 2D image.
• (P/S/C) Improved performance of the copy line (cl) and copy part (cp) commands, primarily when performing on very large images.
• (P/S/C) The 'window' command can place any window type on any position within the image, without limitations of profile or border.
• (E/P/S) For Mac OS, we will only support now the X11 version. Aqua version will be excluded. For OS 10.7, 10.8, and 10.9 X11 versions a boost in performance and stability has been obtained (see here).
• (E/P) Channel selector widget with many channels (menu button) now also show the next and previous buttons for quick switching.
• (E/P) Rearranged the items of the deconvolution menu to fully replicate the deconvolution workflow.
• (P/S) Improved copy/paste and backspace/delete handling in the Huygens Tcl Scripting shell.
• (P/S) Syntax highlighting for the command help displayed in the Task Reports of Huygens Professional.

Bug fixes

• (All) Sometimes the CZI reader failed to read a the pinhole radius and NA properly.
• (All) Fixed a memory leak causing Huygens to crash when deconvolving extremely large datasets under very specific conditions.
• (All) The CZI reader could fail to read very large strings of floats in the meta data, which surpassed regular storage and precission.
• (All) The HDF5 file writer skipped an image if it contained extremely large slices.
• (P/S/C) The window function sometimes created faulty profiles and/or borders.
• (P/S/C) The Lanczos interpolation used by the resample, shift, zoom, isosampling, eqsampling and rotate commands was not supposed to create a wrap-around effect. Yet, this occurred when the shift applied to an image was larger than the Lanczos kernel.
• (P/S/C) MiniMip, hist2Ch en persMip commands are now rejected when the source and destination image are the same instead of creating faulty output.
• (E/P) 3D previews of psf images were shown black due to their low values.
• (E/P) Multimip command did not update all three destination images correctly.
• (E/P) The pinhole spacing was visualized at the pinhole radius parameter in the Optical tab of the main windows.
• (E/P) The workflow of the Deconvolution Wizard for generic/unspecified microscopes is now properly shown.
• (E/P) The resulting thumbnail of an FFT looked awkward when sending the result to the source image.
• (E/P) The Chromatic Shift Corrector blocked the shift vector table until an estimation was carried out. It was actually intended that the user could edit the vectors at any time and correct the image with them.
• (E/P) The template file dialog appended the extension twice if the user removed the suggested name.
• (C) The heuristic SNR estimator (version 1.0) could fail when working with highly clipped images.

4.4 Release (Spring 2013)

All Huygens Products

• Support for the new Zeiss CZI file format in the Full File Format option.
  • CZI files, whether single tiled or multi tiled, can be loaded into Huygens. In the multi tile case the user of Huygens Professional or Huygens Essential will be inquired to select which tiles to open.

Huygens Professional

• New thumbnails in Huygens Professional. Possibility to show them in 3D and twist/tilt them.
• The statistics tabs known from Huygens Essential also available in Huygens Professional.
• New feature to set your own button bar, which is saved in you local preference file. The Icon Selector window can be opened by pressing the grey arrow at the end of the button bar.
• Used new style icons.

(P) New Icon Selector Window

• New feature in Huygens Professional to select your own buttons in the button bar.
• In the icon selector window you can choose all the functionality that can be found in the menu's.
• With search feature to search for specific functions.
• Used the new style icons.
• Extra "Open last" button to open the last opened image.

(E/P) Colocalization Analyzer

• Extended with a mask option. The mask denotes the area to calculate the colocalization coefficients. The GUI is a little adjusted to hold all the options in a structured manner.
• The colocalization coefficients are visualized clearly in a table with sorting functionality.
• The colocalization coefficients choice is stored in your preferences, which means that the last chosen coefficients will be kept.

(E/P) Surface Renderer

• Included a movie tab similar as in the other renderers (MIP, SFP). In this tab you are able to set more animation settings.
• Added the seed slider to get the exact same rendering as in the Object Analyzer.

(E/P) Deconvolution wizard

• New thumbnails also used in the Deconvolution wizard.
• Added the join channels tool in the last stage of the Deconvolution wizard where you can choose which channels/results to combine in a more intuitive manner.

Minor changes

• (E/P) New thumbnails also used in the PSF Distiller wizard.
• (E/P) Added delay feature in the Twin Slicer for the play mode of the slicers, such that you can control how fast the scenes are shown.
• (E/P/S) The Huygens Software accepts _c of _C in filseries for channel configuration, next to the already accepted _ch, _Ch or _CH convention.
• (P/S) The resample commands can be applied to time serie images, where the resampling is applied to each time frame.
• (E/P) The headers and labels in the Microscopic Parameter editor are links to the website giving direct information about a specific parameter.
• (E/P/C) The 'noMetaData' field is accepted in Batch Processor templates.
• (E/P) The thumbnail size is stored in you preferences, such that when starting up the software the last chosen thumbnail size is used.
• (E/P) The Chromatic Shift Corrector can apply more accurate shifts with Lanczos interpolation.
• (C) The analytic (beta) SNR estimator performs better. Also, the thumbnails of the SNR simulations match better the thumbnails of the sample.
• (All) Maximum number of images that can be opened in Huygens Software is increased from 500 to 2000.

Bugfixes

• The Batch Processor yielded slightly different results when executing the same job template. This was due to rounding errors in the FFTW library. This type of error was more exposed when working with the Batch Processor than when working with other tools.
• Improved the required dependencies for the rpm installation packages, such that installation on CentOS, Suse and Red Hat should perform much better.
• Improved visualizing histograms in logarithmic scale, where values of 1 are not correctly shown.
• Removed the blinking of the progress report during deconvolution in Huygens Professional. The progress report is also visible in Huygens Scripting.
• The Chromatic Shift Corrector failed to load packed images.
• The dimensions of a RGB zvi format image are set in the correct order.
• Editing of the tcl shell in Huygens Professional before the command prompt is handled correctly.
• Fixed an initialization problem seldom seen in the Movie Maker when several renderer types where mixed in the loaded movie maker template.
• Disabled the Control-t binding in the tcl shell.
• Used a scroll frame in the cropper, such that widgets that do not fit on screen can be reached with scrolling.
• Rerendering of the twin slicer scenes when hiding the plot.
• Opening a tracks file in the Tracker Analyzer which was previously saved with the Object Tracker could throw an error.

4.3 Release (Fall 2012)

(E/P) New Crosstalk Corrector option

• This new optional tool estimates and corrects channel bleed-through (crosstalk/crossover) for up to 32 different channels automatically.
• Correction is linear and can be applied interactively using the 2D histogram.
• Correction values are plotted in a crosstalk coefficient matrix, which can also be manually adjusted.

New batch Colocalization analysis and histograms creation in Huygens Core

• Added colocalization to the Huygens template readers and task processors. Huygens Core can now compute colocalizaton coefficients and create colocalization maps for pairs of channels in batch mode. A new version of the Huygens Remote Manager will soon be released offering the option to perform colocalization analysis after deconvolution.
• Added 'histogram' task to the Huygens template readers and task processors. Huygens Core can now create 1D/2D histograms in batch mode.

(E/P) STED

• Improved LIF support: parse the LIF type for Pulsed, CW non-gated or CW gated STED.
• Added 'stabilization' stage for STED data to the PSF distiller.
• Improved SNR control in STED deconvolution.
• PSF Distiller supports STED data.
• PSF Distiller estimates STED parameters.

(E/P) Object Tracker

• New analysis type in the Object Tracker for tracking rotation angle and speed.
• Implemented saving and loading track data.
• Possibility to save track detection settings in a template file.
• Added the Track Analyzer to the main menus and pop-up menus.
• Tracker works now more robust with small number of samples or time frames.

(E/P) Twin Slicer

• The line profile within the Twin slicer now updates when slicing through time.
• Added a channel selector to the basic mode of the Twin slicer and in the view mode in Huygens Essential.
• Plot more than one intensity line profile at once in the Twin slicer.
• Remove all arrows and markers from the graph in the Twin Slicer at once, instead of removing them one by one.
• When creating a new intensity profile it is now possible to plot easily along lines parallel to the axes. This can be achieved by pressing 'Shift' while drawing an arbitrary line with the mouse.
• Events previously managed with the 'Ctrl' key are now managed with the 'Shift' key. The Ctrl-LeftMouse is now being used to simulate the Middle Mouse button (see also minor changes).
• The Twin Slicer now shows a "Shortcut Info"-tab explaining all the available shortcuts (key- and mouse-events).

(E/P/S) Usage Report

• New feature: Usage report tool under the Help menu to visualize and list the use of the different Huygens tools.

Minor changes

• (All) One-button mice no longer supported.
• (All) Added possibility to simulate a middle mouse button: 'Ctrl' + 'Left' click.
• (P) Added convert-tools that already existed in Essential to Huygens Professional. Convert, mirror, flip image, which you can find under Tool > Convert...
• (P) New button for quick access to the Batch Processor in Huygens Professional.
• (E/S/C) Report restoration scaling factors. This was only possible in Huygens Professional so far.
• (E/P) The result file of the Chromatic Shift Corrector is now named "....._aligned" instead of "..... _corrected".
• Added 'manual' background mode to the Deconvolution Wizard.
• Backgrounds in byte and integer images are computed with floating point precision. The resulting value is very close to the value obtained by converting the image to floating point prior to background computation.
• (All) New channel selector widget for easy access and control for viewing different channels.
• Much reduced memory usage when generating very large PSFs at negligible accuracy loss.

Bug fixes

• (E/P) The lower threshold slider in the Object Tracker was reset when the upper got enabled and vice versa.
• (E/P) In the Deconvolution Wizard, the template background values were not displayed or taken into account if the user decided to go through the Wizard stages after loading a template.
• (E/P) The MIP renderer threw an error when setting 'Custom colors' if the image had more than 4 channels.
• (All) Applying a negative baseline on byte images, resulted in a wrap around of the negative baseline (e.g. -2 -> 254), which would result in all values to be below zero, which are mapped to 0.
• Add a fallback value for the socket count: 1. This fixes crash issues with virtual machines.
• Reading LSM files often led to an unnecessary scaling (division by 2).
• Files of type ome-xml created with the Bio-formats library could not be opened.

4.2 Release (Spring 2012)

New STED microscope type available in the Huygens suite with astonishing deconvolution results

• Deconvolution of STED datasets.
• Extended LIF file reader with STED parameters.
• New option in the Object Stabilizer to stabilize raw STED data.
• Batch Processor and the Deconvolution Wizard offer option to stabilize STED raw data.
• PSF Distiller supports STED data and also estimates STED parameters.

All products

• Support for very large tiff files (larger than 4 GB, a.k.a BigTiff format). BigTiff uses 64bit offsets.
• New "invertAndOffset" command.

(P/S/C) More filters and commands

• New median and percentile filters.
• New "stabilize" command.

(E/P) New Hot Pixel Remover tool

• This new tool within Huygens Essential (under Tools) and Huygens Professional (under Deconvolution) is a tool to correct for local high intensities, also known as hot pixels.
• Strength estimation to automatically determine the hot pixels.
• Possibility to fine-tune the strength estimation.
• Correct the image (multiple times if you want to compare different settings), where the hot pixel positions are replaced with the median of its neighbourhood.
• Combine information in Z, time or channel direction if you have the knowledge that the hot pixels are at the same position in each slice, timeframe and/or channel.

(E/P) Deconvolution Wizard improvements

• Interactive image comparison and plot tool.
• Improved embedded Twin Slicer.

(E/P) Colocalization Analyzer

• Two additional smart background estimators.

(E) Join Images tool

• The user can now manage and join many images at once.

Minor changes

• (All): The "thres" and "sthres" commands don't need input for every channel now. Missing channel input will be taken from the threshold value of the last entered channel, instead of using default values.
• (E/P): The MIP renderer is now backwards compatible and supports old MIP templates.
• (E/P): Better SFP render efficiency for 2D and 3D (few slices) images.
• (C): HuCore's Batch Processor now finishes jobs successfully even if the preview generation (SFPs, MIPs, etc) fails.
• (C): Performance and thumbnail improvements in the beta SNR estimator.
• (C): HuCore's Batch Processor now accepts empty values in the microscopic templates. Those values, if present, will be fetched from the image metadata, otherwise default values will be used.

Bug fixes

• (All): Limit memory usage and computation time in generating very large PSFs.
• (All): Mac OSX Lion: fix memory problems, workarounds for OSX bugs.
• (All): The Yes/No questions were answered with 'No' if the verbosity level was other than 'normal'.
• (All): Some OME-TIFF files could not be loaded.
• (All): R3D images used to be loaded as time series by default.
• (All): The size of the 'About' window was wrong in some operating systems.
• (All): The "shift" command underperformed in high quality mode, e.g: multichannel packed images, as opposed to multichannel stacked images, were not shifted.
• (E/P): The MIP rendering of 2D images did not work in high-quality mode.
• (E/P): Parsing data for calculating histograms for packed channels is fixed.
• (E/P): The Batch Processor accumulated channels during the deconvolution.
• (E/P): Selecting the custom render size in the SFP renderer and rendering afterwards without typing a custom size raised an error.
• (E/P): The SFP thumbnails would some times appear empty in the Movie Maker.
• (E/P): An error was raised in the Movie Maker if there was an attempt to render the movie as the preview was being played.
• (E/P): The MIP renderer did not downsample the image when needed.
• (E/P): The Movie Maker randomly showed wrong sizes of the MIP thumbnails and previews.
• (E/P): The MIP renderer raised an error when switching channels if a second instance of the renderer was opened.
• (E/P): The main canvas of the MIP renderer would often appear off center (only Mac OS).
• (E/P): A change of the render size in the SFP renderer would lead to the motion mode not working properly.
• (E/P): In the SFP renderer, 'File' -> 'Save scene' mirrored the scene before saving it.

4.1 Release (Fall 2011)

All products

• Color pickers frames: In the entire software a new color picker is used which is better-looking and easier to use.
• A new default color palet is introduced, which is a set of colors that is unambiguous to both color blind people and non-colorblind people.

Operations window in Huygens Pro

• Microscopic parameters and image processing parameters are located in separate notebook tabs.
• Improved menu structure.
• The most frequently used operations can now be accessed through a quick launch button bar.

Maximum Intensity Projection window

• enhanced MIP renderer, with automatic on-the-fly renders and more parameters for customization.

Object analyzer

• The watershed segmentation method is added to the segmentation frame. The seed and garbage level work for the watershed as well.

Object Tracker/Stabilizer

• The cropper version in the tracker and stabilizer is updated.

Object Tracker

• Region of interest (ROI) selection now possible.

Bug fixes

• (All) Lif files with a bit-count between 8 and 16 are now also read properly.
• (All) Improvements when opening images with characters like "[" and "]".
• (E/P) Removed the automatic focus of canvases which would steal the focus of other windows especially in Microsoft Windows.
• (E/P) In the object analyzer it is possible to analyse an empty ROI.
• (E/P) Subimages are now read properly in the batch processor. Only the first subimage was read before.
• (E/P) The deconvolution wizard now stores all settings in the template such that you can reproduce the deconvolution. (bgRadius) This background radius is now also available in the batch processor.
• (E/P) Restarting a wizard stage in the deconvolution wizard is improved.
• (E/P) The SFP renderer did not interpolate several of the parameters when rendering a movie with the embedded movie options.
• (S) The Huygens topSfp command now works with images that are very small in the z-direction.
• (C) In Hucore only the first channel of multichannel images was properly deconvolved when using Huygens Batch templates.

4.0 Release (Spring 2011)

Introduction of a brand new, friendly Huygens Essential user interface Featuring:

• A new deconvolution wizard.
• A step-by-step microscopic parameter wizard.
• Easy access to important image information.
• Quick analysis using the embedded slicer.
• Scalable image thumbnails with individual color settings.
• Tool-widgets for quick image conversions

All products

• Deconvolution is about 20% faster as compared to version 3.7.0.
• Enhanced, faster SFP renderer.
• Enhanced IntelligentCropper is more powerful and easier in use.
• Introduced OME TIFF reader.

(C) HuygensCore

• HuygensCore now supports batch templates which results in a major improvement for the online batch deconvolution tools, such as the Huygens Remote Manager (HRM).
• These batch templates now support thumbnail generation (SFPs, MIPs, stack movies, time movies and MIP comparisons).

(E/P) ObjectTracker

• Improved object detection.
• Detected objects are highlighted using a transparent overlay instead of circles.
• Filter tracks based on the track length, average speed, etc.
• Measure Mean Squared Displacements.
• Create XY, XZ, and YZ velocity scatter plots.
• Measure 2-point velocities instead of 3-point; this gives more reliable measures in case of random motion.
• The plots in Track Analyzer and the data in these plots can be exported to respectively .eps and .csv files.
• Many minor improvements and bug fixes.

(E/P) ObjectStabilizer

• Enhanced rotation detection.

(E/P) ColocalizationAnalyzer

• Much improved GUI with tabbed layout
• Introduction of the RBNCC method (beta).
• Introduction of the Object Spearman colocalization coefficient.

Minor changes

• (E/P) The BatchProcessor allows reading meta data from files besides the use of parameter templates during batch deconvolution.
• (E/P) Improved graphs; measure slopes, enhanced PostScript output.
• (P/S) Tcl and TclHuygens commands that are entered in the shell become hyperlinks to online documentation.
• (P/S/C) Enabled jpeg saving of 2D images through Huygens commands.

Bugfixes

• (All) Fixed some problems in the IPM Tiff reader.
• (All) Added support for Zeiss LSM files larger than 4Gb.
• (E/P) Fixed rendering of 2D images with axial sample density 0.
• (E/P) Fixed creating regions of interest for 2D images in the ObjectAnalyzer.
• (E/P) Fixed high-quality sub-pixel shift in the ObjectStabilizer.

3.7 Release (Fall 2010)

• (E/P) New option: Object Tracker (as beta version available - more features will be added soon)
• (E/P) New option: Chromatic Shift Corrector. This Corrector can estimate and correct for chromatic shifts, fixing the existing misalignments across different channels. The result of this correction is a channel-aligned image free of chromatic shifts. Support for templates is included.
• (E/P) In the Colocalization Analyzer a magnifier has been included to examine the 2D histogram more closely. Thresholds of 1D histograms, 2D histogram and MIP renderer are all linked and all time frames can be analyzed at once. A new Spearman coefficient is also introduced in the Colocalization Analyzer.
• (E/P) In the Object Stabilizer, users can now define a spherical 'Regions Of Interest' in the correlation based stabilization mode. Also an improved tracker is available, plus the option to select and remove tracks. New filters are included to remove outliers, noise (high frequencies), and drift (low frequencies) from displacements.
• (C) A new engine for the Signal to Noise Ratio (SNR) estimator that allows for automatic and accurate SNR determinations of widefield and confocal images of any number of time frames and channels. This new SNR estimator is prepared to work seamlessly with the upcoming release of the Huygens Remote Manager (HRM).

Other changes:

• (P) In the main window of Huygens Professional, a button bar was added with buttons of functions used most often.
• (P) The deconvolution template editor has been improved.
• (E) Templates editor has been updated to store per-channel deconvolution parameters.
• (P) Beta version of a new deconvolution wizard available.
• (P) Enabled possibility to save 2D image as JPEG

3.6 Release (Spring 2010)

• The Huygens Professional now contains a new microscopic parameter wizard. Parameters which are out of normal range will be highlighted and, if possible, corrected.
• The Huygens Essential includes now an Ortho-slicer, which is an extra visualization tool that was only present in the Huygens Professional.
• The Object Analyzer has been renewed and improved. The various manipulation tool sets are better distinguished while analysis choices are made clearer.
• Exporting of data to MATLAB from the Object Analyzer is included now.
• The Colocalization Option now includes an extension of the Pearson coefficient. Like in the intersection coefficient, in the computation of the Object Pearson coefficient, pixels close or below the background are partially or fully excluded from the computation. In this way the Object Pearson coefficient is not biased anymore by large background areas.
• The Object Stabilizer now includes a new option that is meant to stabilize large objects for which cross-correlation did not work due to internal motion.
• The Batch-processor has further improved its scheduling so that shorter deconvolution runs will be finished sooner.
• The LIF fileformat has been renewed to allow the use of very large datasets
• Hyper-thread counting for Intel Core i3, i5, and i7 CPU's is now included. The Huygens Software takes full advantage of hyper-threading and only the 'real' cores are taken into account for the license.
• Reading sampling distances from Nikon ICS files is now fully compatible to the latest Nikon ICS format.

3.5 Release (Autumn 2009)

• The brand new option called the 'Object Stabilizer' (currently in beta) to measure and correct for cell motion, thermal drift, shaking, and other types of movement. It can stabilize and align by means of:
  • cross correlation;
  • object tracking;
  • center-of-mass alignment.
• Optical parameters now also include the coverslip position and the imaging direction for improved handling of spherical aberration, in turn leading to improved deconvolution results.
• A full HDF5 file format reader and writer, now adopted by the Huygens Software as the native open-source file format for images and PSFs. The new format stores all microscopic meta data read by Huygens and includes tags describing the reliability of the meta data.
• Many changes on the graphical interface, resulting in a more modern appearance, reflecting the powerful deconvolution, visualization and analysis capabilities.
• Visualization templates for all our 3D renderers, so you can store your favorite views and reuse them with other datasets.
• Improvements on the Batch Processor:
  • Quicker creation of LIF sub-image jobs.
  • New options for TIFF format output: scaled or clipped results.
• The Colocalization Analyzer can export the 3D colocalization map as an image, or as a new channel to the original stack. You can later take this map into the Object Analyzer for more complex analysis.
• The Object Analyzer contains many new features, like:
  • Interactive thresholds setting on the channel histogram
  • Analysis history that you can save, to reproduce the analysis with the same dataset or reuse with other datasets. This also facilitates batch analysis.
  • Undo mechanism, to quickly revert for example an unfortunate object deletion or filtering.
  • Import analysis and visualization conditions from any other open O.A. instance, so that you can replicate them for different datasets.
  • Render all objects with their accompanying numerical label, for easier analysis reference.
  • Reference 3D cube to know the orientation of the dataset even at large zooms.
  • Cropped datasets can be exported as new channels to the original image, not only overwriting the original ones.
  • Optional on-screen tips to guide you.
  • More possibilities for setting the ROI.
  • More possibilities for selecting anchors, also by filtering the objects based on the reported parameters.
  • Discarded objects and selected anchors are remembered, for the current segmentation parameters, when changing frames in a time series or channels in a pipe.
• Improvements in the SFP renderer:
  • The appearance of the SFP table is now configurable (on/off/mirror).
  • Increased tilt range to 180 degrees, i.e. view from underneath the table.
  • SFP animations are more fluent.
• The Twin- and Ortho Slicer now support multiple rulers and point markers.

Fixes

• Fixes in reading the metadata of Leica LIF files.
• OIF reader updated to support files written with Olympus FluoView 2.x
• Fixes in reading 16 bit LSM files, and improved metadata parser.
• Many other bug fixes.

Patch 3.5.1p2

Some important bugs fixed in the file series reader, Batch Processor, scripting commands, and Object Analyzer.

Patch 3.5.0p4

Bugs fixed in the Object Analyzer, deconvolution with many bricks, and others.

Patch 3.5.0p3

Bug fixed in estimating the background.

Patch 3.5.0p2

Some bugs fixed.

Patch 3.5.0p1

• Essential is able to export microscopic parameters templates again.
• Reporting of parameters after loading a template in Essential's wizard is more readable now.
• The coverslip editor doesn't complain when closing anymore.
• The coverslip position is conveniently updated after cropping the image.
• STK file reading problem in Huygens Core is now fixed.
• In Windows, Huygens Professional couldn't save images that contained colons in their names. This is now fixed.
• In Windows, Huygens could not save files to file servers shared with Samba. This is now fixed.

3.4 Release (Spring 2009)

Patch 3.4.0p1

• Fixed brick artifacts that showed up in confocal images under very large refractive index mismatch, with lens' r.i << medium's r.i.
• Fix for the Movie Maker to render movies in the Intel Mac OS X 10.4 version.

Release 3.4.0p0

• A brand new Movie Maker optional module. This tool allows you to easily create sophisticated animations of your multi-channel 3D images using the powerful Huygens Visualization renderers.
• A HDF5 file format reader.
• A File Series Tool for data selection within large file series.
• Histogram analysis for the columns of the Object Analyzer.
• Speed improvements in the interactivity of the Object Analyzer and the Surface Renderer.
• Scale bars in the Surface Renderer and Fast Mip renderer.
• A button for the Surface Renderer to render in high quality mode before saving the image.
• Enhanced contrast in the overlays in the Twin Slicer and Orthogonal Slicer.
• Fixes in reading the metadata of Zeiss ZVI and Leica LIF files.
• Improvementes on the Batch Processor: allowing saving multidirectory single TIFF files and other fixes.
• Better handling of experimental PSFs in large spherical aberration situations, that previously caused too many bricks.
• The plot command in Huygens Pro can now plot not only functions of one variable in 2D, but also functions of two variables in 3D.

3.3 Release (Fall 2008)

Patch 3.3.2p1

• The Batch Processor can optionally load a whole file series as a single data set, or just each file separately.
• Fixed wrong scaling of integer images after deconvolution in certain cases that generated some negative pixels.
• Fixed slicer pipe in Surface Renderer so that it works with all kinds of data types.
• Improved column statistics reporting in the Object Analyzer .
• Better management of too large objects and memory limitations in the Object Analyzer.
• Implemented new brick modes for the deconvolution commands to handle extreme Spherical Aberrations cases: "one" really forces one brick if memory allows it, "sliceBySlice" goes to the limit of very shallow bricks.
• OME reader/writer updated to OME v1.0 (2008-09).
• Fix in reading large Tiff/LSM files (up to 4 GB on 64 bit systems).
• Fixes in the LIF reader: More reliable way to obtain the sample sizes. Find out if an image is widefield or confocal.
• Fix to avoid a crash in Linux at start up caused by collision with certain X11 libraries.
• Fixes in the Batch Processor to let it run in 32 bit PowerPC Macs.
• Fix in Apple installer for 10.5 to avoid removing the software when re-installing the same version.

Patch 3.3.0p3

• More bugs fixed after the reports of our kind testers, specially in all the new features listed below
• Improvements on the calculation speed of the Object Analyzer (specially noticeable with a few thousands of objects) and some other requests

Patch 3.3.0p2

• Some reported bugs fixed.

Release 3.3.0p1

• The Object Analyzer now offers many new features: new object properties measurements, object filtering, enhanced ROI selection and colocalization analysis. See Object Analyzer.
• Totally renewed Twin Slicer. Synchronized slicing in any orientation, integrated ruler and intensity profile measurement. See Twin Slicer Tutorial.
• Totally renewed Batch Processor. Wizard for task creation, improved handling and editing of templates, support for multi-image files, delayed start timer. Your old templates will be automatically converted. See New Batch Processor Tutorial.
• Totally new Orthogonal Slicer in the Huygens Professional.
• Movie making capabilities for the Surface Renderer.
• New PSF Distiller in Huygens Pro: see New Psf Distiller
• New ZVI file format reader. This will be provided under a new option, together with Biovision IPL (Windows), Biovision IPM (Mac), Leica LIF, Olympus OIF and Zeiss LSM. The ever increasing number of file-formats and frequent changes in the formats themsleves are taking much time from our developers. Therefore using specialized one-brand-only formats will require an option from now on.
• Added Kuwahara to the list of already available restoration filters in Huygens Professional.
• Huygens Professional now has a built-in functions plotter. It can be accessed through the Huygens command 'huOpt plot'.
• Added Debian packages. There are now 4 Linux distro's: x86_64.rpm, i386.rpm, amd64.deb, and i386.deb.
• Linux 3.3 version will be 10% faster than the 3.2 version (this applies to all four basics).
• Plenty of fixed bugs and implemented suggestions from users (thank you for all the feedback!!!)

3.2 Release (Spring 2008)

Supported platforms

• Windows 32 and 64 bit in parallel: Windows NT 4.0, Windows 2000, Windows Server 2003, Windows XP, Windows Vista.
• Apple Mac OS X 10.4 and 10.5, for Intel and PowerPC processors. 32 and 64 bit versions available.
• Linux 32 and 64 bit
• Optional: Itanium and Irix. For these, please Contact Svi.

Patch 3.2.0p7

• Essential will remember the user defined color configuration along sessions
• Fixed a bug that made the program not to be aware of new available versions depending of the version number
• The object analyzer also reports the waist of an object, and the corrected width is used to calculate the aspect ratios.

Release 3.2.0p0

New features

• FreeSFP can directly export animations to AVI files.
• The Object Analyzer
  • Next to center of mass (CM) to CM inter object distances, it is now possible to measure the distance of one object's CM to the surface of a second reference object.
  • More information about the objects in your image, e.g. largest width, location and size of bounding box.
  • A new more convenient display of all measured variables and the measurement conditions
  • More accurate measurement of objects composed of only a few voxels.
• The Colocalization Analyzer:
  • We've removed the h1 and h2 colocalization coefficients from the Colocalization Analyzer because they were too obscure
  • We added the new intersection coefficients, that may be useful in certain circumstances.

• New File Formats:
  • AVI: the Visualization Tools that allow you to create animations can now save them directly to AVI files, apart from still rendering the independent frames as Tiff series.
  • Huygens reads BioVision IPM (.ipm) and Olympus SIS Tiff series.
  • Huygens writes Delta Vision IMSubs (r3d) files.
  • Huygens Core can write JPEG files, facilitating the implementation thumbnails in the Huygens Remote Manager.

• The Huygens Professional slicer remembers the visualization settings for the next time you open it.
• Huygens Pro can now open multiple files in one go: multiple selection is enabled by pressing the Control key while clicking on file names in the Open Dialog.

• The Psf Distiller is now equipped with provisions that will allow the user to specify a reduced size to the final Nipkow PSF in order to use less memory in some limiting cases.
• The Execution Log file remains open all the time now during the program execution, reducing the interference with other operating system utilities monitoring file changes, like Apple's Spotlight.

Bug fixes

Many bugs were fixed in collaboration with users that kindly provided very valuable feedback (kudos to all!!!). For example:

• In the new Huygens Pro, recovery of the old capability of saving in TIFF files in a single file. Also MIP commands are included in the visualization operations.
• Better time out handling in the Batch Processor.
• A workaround for an Apple compiler bug that generated strange deconvolution results, sometimes, in Macs running MacOS X 10.5.
• Improvements in the MacOS X interfaces to increase compatibility.
• A problem in the Batch Processor not properly handling PSF with spaces in the file path.
• Default values for the Signal To Noise Ratio when deconvolving confocal images is now more realistic.
• A bug in the Colocalization Analyzer sometimes rendering a MIP on the image with strange colors.
• Some crashes of the Linux 64 bit version at startup in some machines due to a static linking of the X11 libraries.
• Visualization of an image with an extremely dim channel rendered black sometimes.
• Deconvolving severely undersampled confocal images with measured PSFs sometimes resulted in banding artefacts.
• Edit > Conversions > Data and channel type conversion generated error SubscribeImageCallback.
• Linking different views in the Pro Slicer failed when the image names were too large.
• Errors shown in the Essential interface when handling multi-photon images.
• Some wrong parameter handlings in the Essential wizard when the user goes back to previous steps make the program halt.
• Fix preventing the Batch processor from processing a length-N file series N times.
• Other improvements in the supported File Formats.
  • OME now stores the Microscope Type of the image.
  • Fixed problems reading wavelengths in LSM files with one illumination line per acquisition channel.
  • Fixes in the LIF reader. Improved handling of large LIF files.
  • Fix reading Leica numbered Tiff series, it failed when the number of digits in some counter was not 2.

3.1 Release (Fall 2007)

Patch 3.1.0p1

• Fixes to make the Mac version compatible with MacOSX 10.3.
• Temporary workarounds to make the Mac version compatible with MacOSX 10.5 (until future OS and Frameworks upgrades make these needless).
• Fix to read very large (> 4 GB) LIF files in 64 bit Windows.
• Fix to avoid a cyclic error message when the Twin Slicer was left open during a wizard-guided deconvolution.

Release 3.1.0p0

• After being a 64 bit parallel application for Linux for many years, Huygens will be also available for Windows 64 bit multi core platforms. In 64 bit applications, memory allocation is no longer a problem, no more Not Enough Memory Available messages — provided enough RAM and swap space is available.

• All operations will be stored in an Image History that can be saved along with the files (in ICSfile Format), as text files or as Tcl Huygens scripts to easily automate tasks. The Batch Processor will also save the image history of each task, so you'll always know how your images were restored.
• Improved Tcl Shell for Huygens Professional and Huygens Scripting with the possibility of repeating previous commands, retrieving previous outputs, and expanding image names and Tcl commands.
• Improved usability of the undo mechanism in Huygens Professional.
• Improvements in Huygens Core to facilitate HRM operations. Load a single file in a enumerated series.
• Refined bead rejection criteria in the Psf Distiller.
• When saving to TIFF files you can select between an intensity scaling optimized for visualization purposes (independent channel stretching) or for further analysis (respecting channel ratios, and reporting scaling factors).

• Other improvements in the supported File Formats.
  • Huygens can read user-chosen subimages in LIF files.
  • Better handling of LIF metadata, support for the latest LIF versions.
  • The OMEfile Format writer is fully OME compliant.
  • Time Series written in multi-directory Numbered Tiff series are recognized as such.
  • More portable TIFF files, using a dpi (dots-per-inch) parameter that no longer equals the actaul microscopic sampling but one more appropriate for visualization and printing.
• New File Formats:
  • Huygens reads Olympus OIF file series.
  • Huygens reads IPLab IPL files.
  • BioVision IPM TIFF is supported, but not fully tested.

Bug fixes

Many bugs were fixed in collaboration with users that kindly provided very valuable feedback (kudos to all!!!). For example:

• Some minor but annoying issues in the different user interfaces.
• File name handling is improved to support spaces and international characters in the Batch Processor too.
• Fixed a failure when selecting a very detailed ROI in the Object Analyzer.
• Huygens Essential Interface remained disabled after certain operations.
• Fixed a problem that prevented the deconvolution of very large Time Series
• Fixed a bug that occasionally prevented the resampling of an experimental PSF to be used for images with lower sampling density.
• On multi core machines the Pro Slicer sometimes showed black stripes in the first column of the image

3.0 Release (Spring 2007)

Patch 3.0.0p5

• Fix a bug in the histogram calculator that prevented the Essential Wizard to run with multichannel images

Patch 3.0.0p4

• Disregard irrelevant error in the event queue that prevented deconvolution of large time series
• Fix: error in the isovolume calculation in the object analyzer for very small objects
• Fix a bug in the Pro GUI: Some switches are active by default in the command, but they are marked the other way around in the interface.
• Fix: Old templates can't be found in the new locations.
• Fix: some user preferences (like using the Embedded Memory Manager) do not apply at start up.
• Fix: Essential 'Recent images' list is inactive
• Fix: Large surface renderings are not possible, they are limited to the canvas size
• Batch processor microscopic templates: allow multichannel and edition of a task template.
• Fix: stopping a deconvolution of a large time series doesn't generates an error.
• Improve background estimation for time series

Patch 3.0.0p3

• Embedded Memory Manager improved and enabled for Windows too
• Fix to read some strange formatted LSM files
• Batch Processor bugs fixed:
  • It works in Windows now
  • It works inside the Huygens Professional as well (templates problems fixed)
  • Changing of destination directory fixed

Patch 3.0.0p1

• Some last-minute bugs in the interface of the new Pro Slicer are fixed

Release 3.0.0p0

From this version, all Huygens Software is available for all platforms!!! That means that Huygens Professional is fully revised and is from this moment on also available for native Windows and MacOS X (currently only PowerPC, Intel expected soon). Huygens Essential is again further improved.

New functionality

• Windows and Mac users can now benefit from all the advanced tools in Huygens Professional
• The Pro interface was totally rewritten, and a new powerful Pro Slicer was implemented
• The interactive Batch Processor is incorporated in the Pro as well
• Also the Surface Renderer, Colocalization Analyzer and Object Analyzer options are available under the Pro from now on
• The fixed-view MIP renderer in the older Pro viewer was replaced by the more capable MIP renderer from Essential
• Built-in html browser provides help files for all functions in the Pro that take updated information directly from the SVI-wiki
• Because the sofware is now build natively for Windows it can benefit from multithreading in that platform too, something that until now was only available for other platforms
• A Preferences window lets the users interactively set some common preferences, like default read/write directories

What was kept and improved

• The thumbnail image overview area, but with new, sleeker thumbnails, tooltips, and a pop-up menu to launch render windows
• The Tcl Shell, now equipped with useful keyboard shortcuts like arrow-up to repeat the last command
• The Task report window. Previously this was combined with the Tcl shell in a tabbed deck; now they are simultaneously visible.
• The microscopic parameter edit tab of the older Slicer is replaced by a more informative window.
• The Operations Window, including the new Pro Slicer and the new microscopic parameter edit window.

Fixed bugs

Among other minor bugs, the most noticeable fixes are:

• A bug in the Sfp Renderer that could make the program crash in certain conditions.
• A bug in the Psf Distiller that produced random behavior in the interface in certain conditions (manifested as "too large bead radius").
• A bug in the initialization routine that made the program freeze while automatically checking for updates, if the SVI server was down.
• A bug in the Batch Processor that prevented the restoration of some DeltaVision files.
• Some problems in the interface of the Colocalization Analyzer.
• Difficulties of the Object Analyzer when handling images with empty channels.

2.10 Release (Fall 2006)

New functionalities

• Online help for all the Essential tools. Assistance is also provided in the wizard by text links at the bottom of the info panel. (E)
• Added import and export deconvolution templates to the wizard. (E)
• New file formats:
  • Read and write OME-XML,
  • Read Leica Lif.

Improvements

• Changes in the Psf Distiller to better extract beads and calculate cone angles, reducing also the number of questions to the user.
• The FreeSFP is now included in the Huygens suite and not as an independent distribution.
• Stability and speed improvement of the cropper tool. (E)
• Added support for unsigned short datatype in DeltaVision files.
• Update of the pinhole calculation of Olympus Fluoview Tiff images based on recent reports from the manufacturer.
• Memory improvements:
  • Reading 16 bit tiff images makes integer images in Essential and Batch processor, reducing the memory needs. Scaling is done only when necessary. New -cmode auto for the img open command.
  • Relax resampling criteria in case of OverSampling and resample using less memory.
  • Reduce memory usage by 10% if internal EMM memory manager is disabled
  • Improved Brick Splitting mechanism for the Mac.

Fixed bugs

• Bug in the Sfp Renderer that caused artifacts (slices) under certain illumination conditions.
• Bug in the Psf Distiller occuring when some channels didn't have valid beads (E)
• Batch Processor (E):
  • Batch tasks are quickly killed after user uses Stop button.
  • Errors concerning the PSF are only reported when they will affect the result.
  • Add date and time tag to the file name in the batch processor when output is in tiff format, to reduce the risk of overwritting.
• Handle blank images or channels in deconvolution.
• Improved support for long (up to 128 characters) image names.

Patch release 2.9.1p0 (Summer 2006)

New functionalities

• Leica LIF File Format reader (beta).

Fixed bugs

• Batch Processor task status report.
• Signal To Noise Ratio for QMLE always ended up as infinite in Batch Processor.
• Modification of template values in task lines.
• Fix in TIFF reader, failing at 4-channel images.
• Fix in ICSfileFormat reader, failing at large history track.
• Minor fix in Pro Image Histogram option

Other

• Report scaling of results in the Huygens Essential and the Batch Processor.

2.9 Release (Spring 2006)

General

• File Formats: remote files are now accessed using a more robust buffering method.
• Reduced memory footprint.
• Better handling of multichannel LSM images when many channels were acquired simultaneously.
• Solved bug in exporting the data from user requested histograms.

Huygens Essential

• Batch Processor, a new tool for automatic deconvolution of multiple images.
• QMLE deconvolution algorithm now available through the Batch Processor.
• Object Analyzer, a new tool for Interactive Analysis.
• Many improvements in the Colocalization Analyzer and Surface Renderer tools. New color schemes. R and G colocalization channels simultaneously MIP rendered, for better data thresholding.
• Recently used images list.
• Automatic background estimation now chooses mode appropriate for Microscope Type.
• Improved the structure of the menus.
• Solved bug that produced results different from HuPro's under certain circumstances.

Huygens Professional

• Fixed a race condition at program termination
• Many minor bugs solved.

Huygens Scripting

• New method image borderFill
• Added shift parameter to image createTransfMatrix
• Added HSV support to addMipToSurface and chan2rgba

2.8 Release (Fall 2005)

• Adding a microscopical parameters correction window to the Huygens Essential. It can be launched by right-clicking the image, and choosing "Correct Parameters".
• Adding the ability to address 3 GB on Windows, see our FAQ How can I extend the memory usage on my Windows machine?, to be able to handle much larger image datasets than before on Windows.
• Adding automatic checks for Huygens updates, and an update check button in the "About" window of the Huygens Essential.
• Many improvements in the Colocalization Analyzer and Surface Renderer tools.
• Placing application icons on personal KDE and GNOME desktops.
• Better channels merging in the Psf Distiller wizard.
• Using a faster mathematical library from Intel for the Linux distribution.
• Improving brick-wise restoration of Confocal images with small measured PSF.
• Adding zooming for oversampled big images in the Huygens Essential wizard.
• Coloring the geometry entries in light blue and purple in case of OverSampling.
• Returning the Image Histogram data as Tcl string.
• File Formats:
  • Adding a new file writer: single multi-layer tiff. The user will be now prompted to choose between exporting his data to a tiff file series, or to a single tiff file.
  • Improving the ICS reader to address larger scopes of channels.
  • Improving the Olympus Fluoview microscopical parameters reading.
  • Improvements in the Multi Channel parameters order of the Zeiss LSM reader.
  • Improvements in file series readers which allow importing larger scopes of numbering schemes.
  • Writing the proper geometry notes in the Biorad files, and improving the 16 bit pic reader and writer.

The contents of previous releases are no longer listed

It is with great pleasure that we announce the immediate availability of HRM 3.10.0!

This is a release with various bugfixes that also adds support for Abberior MSR and OBF file formats.

For more detailed information and the included new features, we like to refer you to this website.

HRM 3.10.0 can be downloaded from the official download page: http://huygens-rm.org/wp/?page_id=11.

You can also test our *experimental* new HRM installer! (source http://www.huygens-rm.org)

If you are interested in experiencing the HRM 3.10 userinterface, you can also have a look at http://hrm.svi.nl.